Starting phenix.real_space_refine on Sat Mar 7 15:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.map" model { file = "/net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6v_27223/03_2026/8d6v_27223.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29077 2.51 5 N 8225 2.21 5 O 8966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46380 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "K" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "M" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "N" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Time building chain proxies: 10.42, per 1000 atoms: 0.22 Number of scatterers: 46380 At special positions: 0 Unit cell: (133.4, 136.88, 175.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 8966 8.00 N 8225 7.00 C 29077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11158 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 70 sheets defined 46.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.810A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.552A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.629A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.522A pdb=" N LEU D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.557A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.660A pdb=" N ALA D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.660A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 removed outlier: 3.618A pdb=" N ALA E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.516A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.278A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 removed outlier: 3.538A pdb=" N ALA F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.552A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.183A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 removed outlier: 3.507A pdb=" N LEU I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.383A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.694A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 removed outlier: 3.592A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 removed outlier: 3.617A pdb=" N ALA J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 234 Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.520A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.519A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 removed outlier: 3.594A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.430A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 removed outlier: 3.502A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.592A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.549A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 395 Processing helix chain 'P' and resid 413 through 416 removed outlier: 3.540A pdb=" N SER P 416 " --> pdb=" O ASP P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 413 through 416' Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.871A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.666A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 removed outlier: 3.524A pdb=" N ASN Q 390 " --> pdb=" O MET Q 386 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 396 removed outlier: 3.517A pdb=" N GLN Q 396 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.734A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.631A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 removed outlier: 3.511A pdb=" N ASN R 390 " --> pdb=" O MET R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 395 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.770A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.573A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 removed outlier: 3.523A pdb=" N ASN S 390 " --> pdb=" O MET S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 390 through 397 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.764A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.524A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 389 Processing helix chain 'T' and resid 390 through 396 removed outlier: 3.709A pdb=" N GLN T 396 " --> pdb=" O ALA T 392 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.825A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.678A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 389 Processing helix chain 'U' and resid 390 through 395 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.853A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.648A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 removed outlier: 3.518A pdb=" N ASN V 390 " --> pdb=" O MET V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 390 through 395 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.769A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.681A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 removed outlier: 3.586A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 3.839A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.646A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.706A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.631A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.780A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 removed outlier: 3.635A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 397 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 3.791A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.625A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 removed outlier: 3.511A pdb=" N ASN a 390 " --> pdb=" O MET a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 390 through 395 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.797A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.597A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 removed outlier: 3.504A pdb=" N ASN b 390 " --> pdb=" O MET b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 390 through 395 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.784A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.634A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 395 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.782A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.621A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.610A pdb=" N LEU O 19 " --> pdb=" O GLU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.593A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.669A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.503A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.533A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.482A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.504A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.499A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.515A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.179A pdb=" N ILE H 53 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA H 64 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU H 55 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE H 62 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.488A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.458A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.487A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.559A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 153 through 156 removed outlier: 4.293A pdb=" N VAL M 210 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.498A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.535A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.511A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET P 325 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.780A pdb=" N VAL P 334 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE P 345 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE P 336 " --> pdb=" O THR P 343 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR P 343 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 436 through 440 Processing sheet with id=AD4, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.564A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET Q 325 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 335 removed outlier: 3.720A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AD7, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.651A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.703A pdb=" N VAL R 334 " --> pdb=" O ILE R 345 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE R 345 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE R 336 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR R 343 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE R 420 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE1, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.573A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.703A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 436 through 440 Processing sheet with id=AE4, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.525A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.597A pdb=" N VAL T 334 " --> pdb=" O ILE T 345 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE T 345 " --> pdb=" O VAL T 334 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE T 336 " --> pdb=" O THR T 343 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR T 343 " --> pdb=" O ILE T 336 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AE7, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.531A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.625A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.640A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.517A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.530A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.717A pdb=" N VAL W 334 " --> pdb=" O ILE W 345 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE W 345 " --> pdb=" O VAL W 334 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE W 336 " --> pdb=" O THR W 343 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR W 343 " --> pdb=" O ILE W 336 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.630A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 334 through 335 removed outlier: 3.870A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG1, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.593A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.652A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 436 through 440 Processing sheet with id=AG4, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.425A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE Z 326 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 334 through 335 removed outlier: 3.767A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG7, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.426A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.643A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.558A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.541A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 436 through 440 Processing sheet with id=AH4, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.548A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET c 325 " --> pdb=" O GLN c 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.697A pdb=" N VAL c 334 " --> pdb=" O ILE c 345 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE c 345 " --> pdb=" O VAL c 334 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE c 336 " --> pdb=" O THR c 343 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR c 343 " --> pdb=" O ILE c 336 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.471A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3023 hydrogen bonds defined for protein. 8631 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: 12.87 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12568 1.33 - 1.45: 7877 1.45 - 1.57: 26411 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N THR X 341 " pdb=" CA THR X 341 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.49e+00 bond pdb=" N THR R 341 " pdb=" CA THR R 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N ILE Q 336 " pdb=" CA ILE Q 336 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.20e+00 bond pdb=" N THR Y 341 " pdb=" CA THR Y 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.17e+00 bond pdb=" N THR S 341 " pdb=" CA THR S 341 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.11e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 62515 1.82 - 3.65: 1100 3.65 - 5.47: 84 5.47 - 7.29: 4 7.29 - 9.12: 1 Bond angle restraints: 63704 Sorted by residual: angle pdb=" N ARG O 16 " pdb=" CA ARG O 16 " pdb=" C ARG O 16 " ideal model delta sigma weight residual 112.90 107.75 5.15 1.31e+00 5.83e-01 1.55e+01 angle pdb=" O TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 120.71 124.20 -3.49 9.00e-01 1.23e+00 1.50e+01 angle pdb=" CA PRO R 414 " pdb=" N PRO R 414 " pdb=" CD PRO R 414 " ideal model delta sigma weight residual 112.00 106.72 5.28 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 119.56 117.42 2.14 5.80e-01 2.97e+00 1.36e+01 angle pdb=" N GLY O 66 " pdb=" CA GLY O 66 " pdb=" C GLY O 66 " ideal model delta sigma weight residual 110.29 114.49 -4.20 1.28e+00 6.10e-01 1.08e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 26209 18.10 - 36.19: 1669 36.19 - 54.29: 349 54.29 - 72.39: 60 72.39 - 90.48: 48 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL G 212 " pdb=" C VAL G 212 " pdb=" N LEU G 213 " pdb=" CA LEU G 213 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL H 212 " pdb=" C VAL H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA VAL K 212 " pdb=" C VAL K 212 " pdb=" N LEU K 213 " pdb=" CA LEU K 213 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5570 0.048 - 0.095: 1281 0.095 - 0.143: 387 0.143 - 0.191: 6 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ILE Z 336 " pdb=" N ILE Z 336 " pdb=" C ILE Z 336 " pdb=" CB ILE Z 336 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE Q 336 " pdb=" N ILE Q 336 " pdb=" C ILE Q 336 " pdb=" CB ILE Q 336 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE b 336 " pdb=" N ILE b 336 " pdb=" C ILE b 336 " pdb=" CB ILE b 336 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 413 " 0.086 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO R 414 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 135 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO I 136 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 136 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 136 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 135 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO H 136 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " -0.029 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3898 2.74 - 3.28: 43587 3.28 - 3.82: 76895 3.82 - 4.36: 89776 4.36 - 4.90: 163022 Nonbonded interactions: 377178 Sorted by model distance: nonbonded pdb=" OD1 ASP V 338 " pdb=" OG1 THR V 341 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP W 338 " pdb=" OG1 THR W 341 " model vdw 2.223 3.040 nonbonded pdb=" OG SER Z 422 " pdb=" OE2 GLU Z 432 " model vdw 2.234 3.040 nonbonded pdb=" O ILE E 147 " pdb=" NE2 GLN e 172 " model vdw 2.235 3.120 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.245 3.040 ... (remaining 377173 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 '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' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 3.560 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 45.500 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47066 Z= 0.186 Angle : 0.572 9.118 63704 Z= 0.341 Chirality : 0.044 0.239 7251 Planarity : 0.004 0.128 8400 Dihedral : 13.295 90.483 17177 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.11), residues: 6048 helix: 2.83 (0.10), residues: 2548 sheet: 0.83 (0.13), residues: 1484 loop : 0.06 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 21 TYR 0.021 0.001 TYR M 118 PHE 0.029 0.002 PHE J 71 TRP 0.005 0.001 TRP T 429 HIS 0.005 0.001 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00349 (47066) covalent geometry : angle 0.57179 (63704) hydrogen bonds : bond 0.10488 ( 3023) hydrogen bonds : angle 4.72551 ( 8631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 1.702 Fit side-chains REVERT: A 17 SER cc_start: 0.8552 (m) cc_final: 0.8296 (m) REVERT: A 80 GLN cc_start: 0.8468 (mt0) cc_final: 0.8020 (mt0) REVERT: C 14 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6700 (mtm-85) REVERT: D 174 ASN cc_start: 0.7227 (m-40) cc_final: 0.6593 (t0) REVERT: E 106 THR cc_start: 0.8420 (t) cc_final: 0.7967 (p) REVERT: G 29 SER cc_start: 0.7815 (m) cc_final: 0.7549 (m) REVERT: G 109 THR cc_start: 0.7922 (m) cc_final: 0.7722 (m) REVERT: J 80 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7670 (tp40) REVERT: J 156 MET cc_start: 0.8899 (mtm) cc_final: 0.8603 (mtm) REVERT: K 93 ASP cc_start: 0.8967 (m-30) cc_final: 0.8623 (m-30) REVERT: L 29 SER cc_start: 0.9334 (m) cc_final: 0.9126 (m) REVERT: L 47 SER cc_start: 0.8588 (m) cc_final: 0.8379 (m) REVERT: M 22 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7606 (mtmt) REVERT: R 503 VAL cc_start: 0.8826 (m) cc_final: 0.8527 (p) REVERT: V 354 GLU cc_start: 0.7587 (tt0) cc_final: 0.7265 (tt0) REVERT: X 444 LEU cc_start: 0.8677 (mp) cc_final: 0.8476 (mp) REVERT: Y 458 THR cc_start: 0.8330 (p) cc_final: 0.8053 (p) REVERT: O 93 ASP cc_start: 0.9004 (m-30) cc_final: 0.8785 (m-30) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.2879 time to fit residues: 324.7189 Evaluate side-chains 585 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 0.8980 chunk 597 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN F 216 ASN G 80 GLN I 51 GLN K 105 GLN L 80 GLN M 45 ASN M 80 GLN N 45 ASN P 322 GLN R 322 GLN W 437 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.090512 restraints weight = 53908.885| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.64 r_work: 0.2734 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 47066 Z= 0.223 Angle : 0.574 7.353 63704 Z= 0.302 Chirality : 0.046 0.203 7251 Planarity : 0.005 0.052 8400 Dihedral : 4.013 33.449 6853 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 6.27 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.11), residues: 6048 helix: 2.59 (0.10), residues: 2576 sheet: 0.77 (0.13), residues: 1484 loop : -0.16 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 21 TYR 0.018 0.002 TYR J 87 PHE 0.041 0.003 PHE N 71 TRP 0.006 0.001 TRP b 429 HIS 0.006 0.001 HIS V 365 Details of bonding type rmsd covalent geometry : bond 0.00553 (47066) covalent geometry : angle 0.57357 (63704) hydrogen bonds : bond 0.04783 ( 3023) hydrogen bonds : angle 4.20079 ( 8631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 596 time to evaluate : 1.678 Fit side-chains REVERT: A 17 SER cc_start: 0.8495 (m) cc_final: 0.8292 (m) REVERT: A 114 GLN cc_start: 0.8328 (tp40) cc_final: 0.8052 (tp40) REVERT: D 83 ASP cc_start: 0.8912 (m-30) cc_final: 0.8675 (m-30) REVERT: G 109 THR cc_start: 0.7901 (m) cc_final: 0.7641 (m) REVERT: H 44 GLU cc_start: 0.7442 (pt0) cc_final: 0.7237 (pt0) REVERT: H 73 ASN cc_start: 0.8139 (t0) cc_final: 0.7587 (m-40) REVERT: H 143 TYR cc_start: 0.7634 (p90) cc_final: 0.7277 (p90) REVERT: H 144 ASP cc_start: 0.7058 (p0) cc_final: 0.6751 (p0) REVERT: H 156 MET cc_start: 0.8079 (mtm) cc_final: 0.7378 (mtm) REVERT: H 225 ILE cc_start: 0.8202 (mt) cc_final: 0.7557 (tp) REVERT: I 51 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6288 (mt0) REVERT: I 209 GLU cc_start: 0.7087 (tt0) cc_final: 0.6648 (tt0) REVERT: J 26 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7582 (mtm110) REVERT: J 80 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8229 (tp40) REVERT: L 11 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6720 (tp40) REVERT: L 156 MET cc_start: 0.8851 (mtm) cc_final: 0.8440 (mtm) REVERT: M 105 GLN cc_start: 0.8218 (mt0) cc_final: 0.7976 (mm-40) REVERT: N 14 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7107 (ttp-110) REVERT: N 24 ILE cc_start: 0.8722 (mm) cc_final: 0.8309 (mt) REVERT: N 173 GLU cc_start: 0.7732 (mp0) cc_final: 0.7348 (mm-30) REVERT: Q 314 MET cc_start: 0.9102 (ttt) cc_final: 0.8825 (ttt) REVERT: Y 314 MET cc_start: 0.9161 (ttt) cc_final: 0.8894 (ttt) REVERT: Y 338 ASP cc_start: 0.8324 (t0) cc_final: 0.8120 (t70) REVERT: Z 338 ASP cc_start: 0.8498 (t70) cc_final: 0.8290 (t70) REVERT: b 338 ASP cc_start: 0.8353 (t0) cc_final: 0.8126 (t0) REVERT: O 114 GLN cc_start: 0.8621 (mt0) cc_final: 0.8286 (mt0) outliers start: 47 outliers final: 36 residues processed: 615 average time/residue: 0.2825 time to fit residues: 285.0566 Evaluate side-chains 600 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 563 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 519 GLU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 509 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 486 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.0030 chunk 297 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 517 optimal weight: 3.9990 chunk 485 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN I 51 GLN K 165 ASN L 80 GLN N 45 ASN P 322 GLN T 324 ASN U 324 ASN ** Y 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093754 restraints weight = 53276.030| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.63 r_work: 0.2797 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 47066 Z= 0.101 Angle : 0.451 6.904 63704 Z= 0.243 Chirality : 0.042 0.170 7251 Planarity : 0.003 0.048 8400 Dihedral : 3.668 29.817 6853 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.97 % Allowed : 8.21 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.11), residues: 6048 helix: 2.93 (0.10), residues: 2576 sheet: 0.79 (0.13), residues: 1526 loop : -0.01 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 21 TYR 0.008 0.001 TYR H 35 PHE 0.033 0.002 PHE N 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00223 (47066) covalent geometry : angle 0.45051 (63704) hydrogen bonds : bond 0.03392 ( 3023) hydrogen bonds : angle 3.97659 ( 8631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 584 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8453 (m) cc_final: 0.8236 (m) REVERT: A 156 MET cc_start: 0.8893 (mtm) cc_final: 0.8406 (mtm) REVERT: D 174 ASN cc_start: 0.6987 (m-40) cc_final: 0.6771 (m110) REVERT: E 105 GLN cc_start: 0.7650 (tp40) cc_final: 0.7321 (tp40) REVERT: E 154 VAL cc_start: 0.7070 (t) cc_final: 0.6861 (p) REVERT: G 109 THR cc_start: 0.7832 (m) cc_final: 0.7575 (m) REVERT: H 14 ARG cc_start: 0.5759 (mtm180) cc_final: 0.5543 (mtm180) REVERT: H 143 TYR cc_start: 0.7295 (p90) cc_final: 0.6983 (p90) REVERT: J 26 ARG cc_start: 0.7571 (mtm110) cc_final: 0.7329 (mtm110) REVERT: J 80 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8221 (tp40) REVERT: L 11 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6657 (tp40) REVERT: L 156 MET cc_start: 0.8830 (mtm) cc_final: 0.8457 (mtm) REVERT: M 22 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7341 (mtmt) REVERT: M 165 ASN cc_start: 0.7681 (m-40) cc_final: 0.7453 (m110) REVERT: N 14 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7111 (ttp-110) REVERT: N 24 ILE cc_start: 0.8572 (mm) cc_final: 0.8074 (mt) REVERT: N 45 ASN cc_start: 0.8630 (t0) cc_final: 0.8349 (t0) REVERT: N 173 GLU cc_start: 0.7797 (mp0) cc_final: 0.7410 (mm-30) REVERT: S 395 MET cc_start: 0.7152 (mmt) cc_final: 0.6945 (mmm) REVERT: X 322 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: Z 364 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8436 (tp30) outliers start: 45 outliers final: 30 residues processed: 601 average time/residue: 0.2763 time to fit residues: 274.6371 Evaluate side-chains 589 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 557 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 430 ASN Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 414 optimal weight: 8.9990 chunk 470 optimal weight: 2.9990 chunk 407 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 555 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 268 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN P 322 GLN S 390 ASN U 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.091364 restraints weight = 53593.256| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.64 r_work: 0.2749 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 47066 Z= 0.161 Angle : 0.496 6.527 63704 Z= 0.265 Chirality : 0.043 0.187 7251 Planarity : 0.004 0.046 8400 Dihedral : 3.786 30.169 6853 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.34 % Allowed : 9.33 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.11), residues: 6048 helix: 2.85 (0.10), residues: 2576 sheet: 0.75 (0.13), residues: 1526 loop : -0.09 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 182 TYR 0.011 0.001 TYR J 87 PHE 0.033 0.003 PHE J 71 TRP 0.005 0.001 TRP T 429 HIS 0.005 0.001 HIS S 365 Details of bonding type rmsd covalent geometry : bond 0.00390 (47066) covalent geometry : angle 0.49559 (63704) hydrogen bonds : bond 0.04073 ( 3023) hydrogen bonds : angle 3.99673 ( 8631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 579 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8471 (m) cc_final: 0.8255 (m) REVERT: A 24 ILE cc_start: 0.7910 (mm) cc_final: 0.7515 (mt) REVERT: D 28 LYS cc_start: 0.7435 (mmtm) cc_final: 0.7183 (mmtp) REVERT: G 29 SER cc_start: 0.7859 (OUTLIER) cc_final: 0.7593 (m) REVERT: G 109 THR cc_start: 0.7839 (m) cc_final: 0.7608 (m) REVERT: H 73 ASN cc_start: 0.8068 (t0) cc_final: 0.7592 (m-40) REVERT: H 143 TYR cc_start: 0.7483 (p90) cc_final: 0.7135 (p90) REVERT: H 144 ASP cc_start: 0.6980 (p0) cc_final: 0.6530 (p0) REVERT: J 26 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7335 (mtm110) REVERT: J 80 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8264 (tp40) REVERT: J 156 MET cc_start: 0.9197 (mtm) cc_final: 0.8861 (mtm) REVERT: L 11 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6687 (tp40) REVERT: L 156 MET cc_start: 0.8875 (mtm) cc_final: 0.8482 (mtm) REVERT: M 105 GLN cc_start: 0.8195 (mt0) cc_final: 0.7945 (mm-40) REVERT: M 171 TYR cc_start: 0.7665 (t80) cc_final: 0.7408 (t80) REVERT: N 14 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7049 (ttp-110) REVERT: N 24 ILE cc_start: 0.8628 (mm) cc_final: 0.8202 (mt) REVERT: N 45 ASN cc_start: 0.8649 (t0) cc_final: 0.8355 (t0) REVERT: N 173 GLU cc_start: 0.7840 (mp0) cc_final: 0.7450 (mm-30) REVERT: S 395 MET cc_start: 0.7116 (mmt) cc_final: 0.6904 (mmm) REVERT: X 345 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8949 (mm) REVERT: Y 338 ASP cc_start: 0.8347 (t0) cc_final: 0.8073 (t0) REVERT: Y 390 ASN cc_start: 0.8772 (t0) cc_final: 0.8528 (t0) REVERT: Z 364 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: a 324 ASN cc_start: 0.8365 (m-40) cc_final: 0.8126 (m-40) REVERT: b 338 ASP cc_start: 0.8460 (t0) cc_final: 0.8210 (t0) outliers start: 62 outliers final: 54 residues processed: 601 average time/residue: 0.2821 time to fit residues: 278.2498 Evaluate side-chains 611 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 554 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 17 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 292 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 561 optimal weight: 4.9990 chunk 443 optimal weight: 1.9990 chunk 372 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 423 optimal weight: 0.0070 chunk 389 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 424 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN H 11 GLN K 231 GLN P 322 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.093308 restraints weight = 53212.407| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.63 r_work: 0.2783 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 47066 Z= 0.104 Angle : 0.445 6.043 63704 Z= 0.240 Chirality : 0.042 0.169 7251 Planarity : 0.003 0.044 8400 Dihedral : 3.623 27.245 6853 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.21 % Allowed : 10.22 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.11), residues: 6048 helix: 2.99 (0.10), residues: 2590 sheet: 0.84 (0.13), residues: 1526 loop : -0.04 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 182 TYR 0.009 0.001 TYR b 359 PHE 0.031 0.002 PHE A 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00236 (47066) covalent geometry : angle 0.44479 (63704) hydrogen bonds : bond 0.03360 ( 3023) hydrogen bonds : angle 3.89691 ( 8631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 570 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8536 (m) cc_final: 0.8307 (m) REVERT: D 28 LYS cc_start: 0.7456 (mmtm) cc_final: 0.7206 (mmtp) REVERT: D 174 ASN cc_start: 0.7004 (m-40) cc_final: 0.6772 (m110) REVERT: E 105 GLN cc_start: 0.7662 (tp40) cc_final: 0.7302 (tp40) REVERT: E 140 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7195 (mtm110) REVERT: G 29 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7580 (m) REVERT: G 109 THR cc_start: 0.7815 (m) cc_final: 0.7576 (m) REVERT: H 156 MET cc_start: 0.7860 (mtm) cc_final: 0.7329 (mtm) REVERT: J 26 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7249 (mtm110) REVERT: J 80 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8209 (tp40) REVERT: J 233 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7539 (tp) REVERT: K 10 GLU cc_start: 0.7219 (tp30) cc_final: 0.6914 (tm-30) REVERT: L 11 GLN cc_start: 0.6887 (tm-30) cc_final: 0.6667 (tp40) REVERT: L 156 MET cc_start: 0.8867 (mtm) cc_final: 0.8491 (mtm) REVERT: M 22 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7559 (mtmt) REVERT: M 165 ASN cc_start: 0.7741 (m-40) cc_final: 0.7480 (m110) REVERT: N 14 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7142 (ttp-110) REVERT: N 24 ILE cc_start: 0.8535 (mm) cc_final: 0.8081 (mt) REVERT: N 167 LEU cc_start: 0.7784 (mt) cc_final: 0.7581 (mt) REVERT: N 173 GLU cc_start: 0.7812 (mp0) cc_final: 0.7426 (mm-30) REVERT: S 395 MET cc_start: 0.7133 (mmt) cc_final: 0.6925 (mmm) REVERT: X 322 GLN cc_start: 0.8294 (pm20) cc_final: 0.8082 (pm20) REVERT: X 345 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8914 (mm) REVERT: Y 338 ASP cc_start: 0.8242 (t0) cc_final: 0.8009 (t0) REVERT: Y 390 ASN cc_start: 0.8690 (t0) cc_final: 0.8434 (t0) REVERT: Y 415 GLN cc_start: 0.8151 (mm110) cc_final: 0.7936 (mm-40) REVERT: Y 432 GLU cc_start: 0.7514 (tp30) cc_final: 0.7225 (tp30) REVERT: Y 434 GLU cc_start: 0.7837 (pt0) cc_final: 0.7614 (pt0) REVERT: Z 364 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (tp30) REVERT: a 324 ASN cc_start: 0.8326 (m-40) cc_final: 0.8105 (m-40) REVERT: b 338 ASP cc_start: 0.8293 (t0) cc_final: 0.8033 (t0) REVERT: O 134 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7820 (ttpp) REVERT: O 183 ILE cc_start: 0.7811 (mt) cc_final: 0.7572 (mt) outliers start: 56 outliers final: 44 residues processed: 594 average time/residue: 0.2397 time to fit residues: 235.7365 Evaluate side-chains 606 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 558 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 447 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 596 optimal weight: 5.9990 chunk 56 optimal weight: 0.0570 chunk 171 optimal weight: 1.9990 chunk 589 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 337 optimal weight: 0.8980 chunk 487 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 375 optimal weight: 3.9990 chunk 467 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 165 ASN P 322 GLN S 390 ASN U 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN O 231 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.093378 restraints weight = 53428.324| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.62 r_work: 0.2776 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 47066 Z= 0.111 Angle : 0.448 6.419 63704 Z= 0.241 Chirality : 0.042 0.172 7251 Planarity : 0.003 0.043 8400 Dihedral : 3.579 24.337 6853 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.27 % Allowed : 10.75 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.11), residues: 6048 helix: 3.03 (0.10), residues: 2590 sheet: 0.86 (0.13), residues: 1526 loop : -0.03 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 182 TYR 0.009 0.001 TYR Z 359 PHE 0.031 0.002 PHE I 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 Details of bonding type rmsd covalent geometry : bond 0.00259 (47066) covalent geometry : angle 0.44751 (63704) hydrogen bonds : bond 0.03396 ( 3023) hydrogen bonds : angle 3.86045 ( 8631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 568 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8529 (m) cc_final: 0.8305 (m) REVERT: A 24 ILE cc_start: 0.7812 (mm) cc_final: 0.7429 (mt) REVERT: D 28 LYS cc_start: 0.7387 (mmtm) cc_final: 0.7129 (mmtp) REVERT: D 174 ASN cc_start: 0.6994 (m-40) cc_final: 0.6776 (m110) REVERT: E 105 GLN cc_start: 0.7673 (tp40) cc_final: 0.7295 (tp40) REVERT: E 140 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7214 (mtm110) REVERT: G 29 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7659 (m) REVERT: G 109 THR cc_start: 0.7798 (m) cc_final: 0.7555 (m) REVERT: H 156 MET cc_start: 0.7925 (mtm) cc_final: 0.7294 (mtm) REVERT: J 80 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8311 (tt0) REVERT: J 233 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (tp) REVERT: K 10 GLU cc_start: 0.7154 (tp30) cc_final: 0.6843 (tm-30) REVERT: L 11 GLN cc_start: 0.6809 (tm-30) cc_final: 0.6583 (tp40) REVERT: L 156 MET cc_start: 0.8875 (mtm) cc_final: 0.8513 (mtm) REVERT: N 14 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7133 (ttp-110) REVERT: N 24 ILE cc_start: 0.8543 (mm) cc_final: 0.8092 (mt) REVERT: N 173 GLU cc_start: 0.7827 (mp0) cc_final: 0.7422 (mm-30) REVERT: S 395 MET cc_start: 0.7112 (mmt) cc_final: 0.6894 (mmm) REVERT: X 345 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8932 (mm) REVERT: Y 338 ASP cc_start: 0.8305 (t0) cc_final: 0.8059 (t0) REVERT: Y 390 ASN cc_start: 0.8691 (t0) cc_final: 0.8435 (t0) REVERT: Y 415 GLN cc_start: 0.8137 (mm110) cc_final: 0.7929 (mm-40) REVERT: Z 364 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: a 324 ASN cc_start: 0.8303 (m-40) cc_final: 0.8045 (m-40) REVERT: b 338 ASP cc_start: 0.8237 (t0) cc_final: 0.8014 (t0) REVERT: O 22 LYS cc_start: 0.7972 (mttt) cc_final: 0.7750 (mttt) REVERT: O 183 ILE cc_start: 0.7856 (mt) cc_final: 0.7635 (mt) outliers start: 59 outliers final: 51 residues processed: 590 average time/residue: 0.2359 time to fit residues: 229.6445 Evaluate side-chains 610 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 555 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 320 SER Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 390 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 379 optimal weight: 0.0060 chunk 476 optimal weight: 0.8980 chunk 485 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 295 optimal weight: 0.7980 chunk 439 optimal weight: 0.7980 chunk 579 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN G 80 GLN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.094045 restraints weight = 53137.785| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.62 r_work: 0.2793 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 47066 Z= 0.100 Angle : 0.438 7.023 63704 Z= 0.236 Chirality : 0.042 0.168 7251 Planarity : 0.003 0.047 8400 Dihedral : 3.520 21.464 6853 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.36 % Allowed : 11.23 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.11), residues: 6048 helix: 3.09 (0.10), residues: 2590 sheet: 0.90 (0.13), residues: 1526 loop : 0.00 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 26 TYR 0.009 0.001 TYR Z 359 PHE 0.030 0.002 PHE I 71 TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00226 (47066) covalent geometry : angle 0.43808 (63704) hydrogen bonds : bond 0.03209 ( 3023) hydrogen bonds : angle 3.83332 ( 8631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 570 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8545 (m) cc_final: 0.8321 (m) REVERT: D 28 LYS cc_start: 0.7395 (mmtm) cc_final: 0.7144 (mmtp) REVERT: D 174 ASN cc_start: 0.6991 (m-40) cc_final: 0.6771 (m110) REVERT: E 105 GLN cc_start: 0.7632 (tp40) cc_final: 0.7244 (tp40) REVERT: E 140 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7196 (mtm110) REVERT: G 29 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7589 (m) REVERT: G 109 THR cc_start: 0.7833 (m) cc_final: 0.7573 (m) REVERT: H 156 MET cc_start: 0.7906 (mtm) cc_final: 0.7169 (mtm) REVERT: H 167 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5511 (mp) REVERT: I 135 ARG cc_start: 0.7731 (ptm160) cc_final: 0.6975 (mmm-85) REVERT: J 80 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8305 (tt0) REVERT: J 233 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7522 (tp) REVERT: K 10 GLU cc_start: 0.7165 (tp30) cc_final: 0.6865 (tm-30) REVERT: L 11 GLN cc_start: 0.6842 (tm-30) cc_final: 0.6582 (tp40) REVERT: L 156 MET cc_start: 0.8874 (mtm) cc_final: 0.8501 (mtm) REVERT: N 14 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7148 (ttp-110) REVERT: N 24 ILE cc_start: 0.8514 (mm) cc_final: 0.8059 (mt) REVERT: N 173 GLU cc_start: 0.7814 (mp0) cc_final: 0.7419 (mm-30) REVERT: S 395 MET cc_start: 0.7117 (mmt) cc_final: 0.6904 (mmm) REVERT: W 367 GLU cc_start: 0.8755 (tt0) cc_final: 0.8517 (tt0) REVERT: X 345 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8919 (mm) REVERT: Y 338 ASP cc_start: 0.8285 (t0) cc_final: 0.8046 (t0) REVERT: Y 390 ASN cc_start: 0.8643 (t0) cc_final: 0.8374 (t0) REVERT: Y 415 GLN cc_start: 0.8128 (mm110) cc_final: 0.7918 (mm-40) REVERT: Y 432 GLU cc_start: 0.7483 (tp30) cc_final: 0.7078 (tp30) REVERT: Z 364 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: a 324 ASN cc_start: 0.8274 (m-40) cc_final: 0.8015 (m-40) REVERT: O 22 LYS cc_start: 0.7956 (mttt) cc_final: 0.7736 (mttt) outliers start: 63 outliers final: 49 residues processed: 599 average time/residue: 0.1987 time to fit residues: 197.0842 Evaluate side-chains 607 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 553 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 320 SER Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 339 ASP Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 28 optimal weight: 4.9990 chunk 588 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 273 optimal weight: 0.7980 chunk 524 optimal weight: 1.9990 chunk 492 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 568 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN G 80 GLN I 51 GLN P 322 GLN S 390 ASN T 324 ASN Y 322 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.092113 restraints weight = 53595.534| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.64 r_work: 0.2763 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 47066 Z= 0.146 Angle : 0.483 9.013 63704 Z= 0.257 Chirality : 0.043 0.181 7251 Planarity : 0.003 0.052 8400 Dihedral : 3.658 21.817 6853 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.34 % Allowed : 11.49 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.11), residues: 6048 helix: 2.97 (0.10), residues: 2590 sheet: 0.85 (0.13), residues: 1526 loop : -0.08 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 26 TYR 0.010 0.001 TYR N 171 PHE 0.032 0.002 PHE I 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 Details of bonding type rmsd covalent geometry : bond 0.00354 (47066) covalent geometry : angle 0.48277 (63704) hydrogen bonds : bond 0.03762 ( 3023) hydrogen bonds : angle 3.89980 ( 8631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 564 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8551 (m) cc_final: 0.8334 (m) REVERT: A 24 ILE cc_start: 0.7926 (mm) cc_final: 0.7532 (mt) REVERT: D 174 ASN cc_start: 0.6962 (m-40) cc_final: 0.6746 (m110) REVERT: E 105 GLN cc_start: 0.7671 (tp40) cc_final: 0.7285 (tp40) REVERT: E 140 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7228 (mtm110) REVERT: E 156 MET cc_start: 0.8284 (mtm) cc_final: 0.7843 (mtm) REVERT: G 109 THR cc_start: 0.7853 (m) cc_final: 0.7615 (m) REVERT: H 73 ASN cc_start: 0.8039 (t0) cc_final: 0.7569 (m-40) REVERT: H 144 ASP cc_start: 0.6997 (p0) cc_final: 0.6738 (p0) REVERT: H 167 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5593 (mp) REVERT: I 135 ARG cc_start: 0.7733 (ptm160) cc_final: 0.6971 (mmm-85) REVERT: J 80 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8340 (tt0) REVERT: J 233 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7501 (tp) REVERT: K 10 GLU cc_start: 0.7208 (tp30) cc_final: 0.6890 (tm-30) REVERT: L 11 GLN cc_start: 0.6837 (tm-30) cc_final: 0.6575 (tp40) REVERT: L 156 MET cc_start: 0.8922 (mtm) cc_final: 0.8558 (mtm) REVERT: M 165 ASN cc_start: 0.7753 (m-40) cc_final: 0.7540 (m110) REVERT: N 24 ILE cc_start: 0.8573 (mm) cc_final: 0.8180 (mt) REVERT: N 173 GLU cc_start: 0.7828 (mp0) cc_final: 0.7425 (mm-30) REVERT: X 322 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: X 345 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8941 (mm) REVERT: Y 338 ASP cc_start: 0.8290 (t0) cc_final: 0.8063 (t0) REVERT: Y 390 ASN cc_start: 0.8664 (t0) cc_final: 0.8419 (t0) REVERT: Y 415 GLN cc_start: 0.8133 (mm110) cc_final: 0.7930 (mm-40) REVERT: Y 432 GLU cc_start: 0.7412 (tp30) cc_final: 0.7077 (tp30) REVERT: Z 364 GLU cc_start: 0.8635 (tt0) cc_final: 0.8379 (tp30) REVERT: a 324 ASN cc_start: 0.8317 (m-40) cc_final: 0.8065 (m-40) REVERT: a 390 ASN cc_start: 0.8595 (t0) cc_final: 0.8208 (t0) REVERT: b 338 ASP cc_start: 0.8428 (t0) cc_final: 0.8117 (t70) REVERT: O 114 GLN cc_start: 0.8566 (mt0) cc_final: 0.8255 (mt0) outliers start: 62 outliers final: 53 residues processed: 591 average time/residue: 0.1744 time to fit residues: 172.1476 Evaluate side-chains 612 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 555 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 320 SER Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 437 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 467 optimal weight: 2.9990 chunk 440 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 584 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 564 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN G 80 GLN G 174 ASN I 51 GLN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092790 restraints weight = 53497.390| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.64 r_work: 0.2772 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 47066 Z= 0.118 Angle : 0.464 9.208 63704 Z= 0.247 Chirality : 0.042 0.173 7251 Planarity : 0.003 0.059 8400 Dihedral : 3.606 21.614 6853 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.27 % Allowed : 11.83 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.11), residues: 6048 helix: 3.04 (0.10), residues: 2590 sheet: 0.87 (0.13), residues: 1526 loop : -0.05 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 26 TYR 0.009 0.001 TYR N 171 PHE 0.031 0.002 PHE I 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS b 365 Details of bonding type rmsd covalent geometry : bond 0.00276 (47066) covalent geometry : angle 0.46433 (63704) hydrogen bonds : bond 0.03475 ( 3023) hydrogen bonds : angle 3.88150 ( 8631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 562 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8531 (m) cc_final: 0.8305 (m) REVERT: A 24 ILE cc_start: 0.7831 (mm) cc_final: 0.7469 (mt) REVERT: D 174 ASN cc_start: 0.6941 (m-40) cc_final: 0.6730 (m110) REVERT: E 105 GLN cc_start: 0.7667 (tp40) cc_final: 0.7280 (tp40) REVERT: E 140 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7351 (mtm110) REVERT: E 156 MET cc_start: 0.8272 (mtm) cc_final: 0.7807 (mtm) REVERT: F 111 PHE cc_start: 0.7328 (t80) cc_final: 0.6832 (t80) REVERT: G 109 THR cc_start: 0.7788 (m) cc_final: 0.7545 (m) REVERT: H 73 ASN cc_start: 0.8017 (t0) cc_final: 0.7557 (m-40) REVERT: H 156 MET cc_start: 0.7889 (mtm) cc_final: 0.7546 (mtm) REVERT: H 167 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5543 (mp) REVERT: I 135 ARG cc_start: 0.7734 (ptm160) cc_final: 0.6956 (mmm-85) REVERT: J 80 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8325 (tt0) REVERT: K 10 GLU cc_start: 0.7144 (tp30) cc_final: 0.6814 (tm-30) REVERT: L 11 GLN cc_start: 0.6810 (tm-30) cc_final: 0.6547 (tp40) REVERT: L 156 MET cc_start: 0.8915 (mtm) cc_final: 0.8539 (mtm) REVERT: M 105 GLN cc_start: 0.8146 (mt0) cc_final: 0.7899 (mm-40) REVERT: M 165 ASN cc_start: 0.7708 (m-40) cc_final: 0.7475 (m110) REVERT: N 24 ILE cc_start: 0.8532 (mm) cc_final: 0.8135 (mt) REVERT: N 173 GLU cc_start: 0.7964 (mp0) cc_final: 0.7522 (mm-30) REVERT: W 367 GLU cc_start: 0.8794 (tt0) cc_final: 0.8571 (tt0) REVERT: X 322 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: X 345 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (mm) REVERT: Y 338 ASP cc_start: 0.8291 (t0) cc_final: 0.8049 (t0) REVERT: Y 390 ASN cc_start: 0.8651 (t0) cc_final: 0.8428 (t0) REVERT: Y 415 GLN cc_start: 0.8133 (mm110) cc_final: 0.7927 (mm-40) REVERT: Y 432 GLU cc_start: 0.7441 (tp30) cc_final: 0.7179 (tp30) REVERT: Z 364 GLU cc_start: 0.8605 (tt0) cc_final: 0.8354 (tp30) REVERT: a 324 ASN cc_start: 0.8294 (m-40) cc_final: 0.8033 (m-40) REVERT: a 390 ASN cc_start: 0.8606 (t0) cc_final: 0.8220 (t0) REVERT: O 22 LYS cc_start: 0.7971 (mttt) cc_final: 0.7742 (mttt) REVERT: O 183 ILE cc_start: 0.7736 (mt) cc_final: 0.7526 (mt) outliers start: 59 outliers final: 52 residues processed: 587 average time/residue: 0.1703 time to fit residues: 166.9037 Evaluate side-chains 604 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 549 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 320 SER Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 399 LEU Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 399 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.0170 chunk 509 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 543 optimal weight: 0.7980 chunk 364 optimal weight: 0.6980 chunk 446 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 485 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.093731 restraints weight = 53414.421| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.63 r_work: 0.2782 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 47066 Z= 0.105 Angle : 0.452 9.144 63704 Z= 0.241 Chirality : 0.042 0.172 7251 Planarity : 0.003 0.060 8400 Dihedral : 3.533 21.092 6853 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.25 % Allowed : 11.90 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.11), residues: 6048 helix: 3.12 (0.10), residues: 2576 sheet: 0.89 (0.13), residues: 1526 loop : 0.02 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 26 TYR 0.012 0.001 TYR N 130 PHE 0.031 0.002 PHE I 71 TRP 0.004 0.001 TRP T 429 HIS 0.003 0.001 HIS a 365 Details of bonding type rmsd covalent geometry : bond 0.00242 (47066) covalent geometry : angle 0.45235 (63704) hydrogen bonds : bond 0.03250 ( 3023) hydrogen bonds : angle 3.84722 ( 8631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 552 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8564 (m) cc_final: 0.8339 (m) REVERT: D 174 ASN cc_start: 0.6955 (m-40) cc_final: 0.6736 (m110) REVERT: E 140 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7225 (mtm110) REVERT: G 109 THR cc_start: 0.7843 (m) cc_final: 0.7587 (m) REVERT: H 167 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5546 (mp) REVERT: I 135 ARG cc_start: 0.7737 (ptm160) cc_final: 0.6978 (mmm-85) REVERT: J 80 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8310 (tt0) REVERT: L 11 GLN cc_start: 0.6839 (tm-30) cc_final: 0.6584 (tp40) REVERT: L 156 MET cc_start: 0.8925 (mtm) cc_final: 0.8560 (mtm) REVERT: M 105 GLN cc_start: 0.8136 (mt0) cc_final: 0.7894 (mm-40) REVERT: M 165 ASN cc_start: 0.7746 (m-40) cc_final: 0.7411 (m110) REVERT: M 214 ASP cc_start: 0.7615 (t70) cc_final: 0.7183 (p0) REVERT: N 24 ILE cc_start: 0.8528 (mm) cc_final: 0.8085 (mt) REVERT: N 173 GLU cc_start: 0.7859 (mp0) cc_final: 0.7428 (mm-30) REVERT: X 322 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: X 345 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8917 (mm) REVERT: Y 390 ASN cc_start: 0.8624 (t0) cc_final: 0.8410 (t0) REVERT: Y 415 GLN cc_start: 0.8117 (mm110) cc_final: 0.7914 (mm-40) REVERT: Y 432 GLU cc_start: 0.7391 (tp30) cc_final: 0.7147 (tp30) REVERT: Z 364 GLU cc_start: 0.8499 (tt0) cc_final: 0.8237 (tp30) REVERT: a 324 ASN cc_start: 0.8217 (m-40) cc_final: 0.7982 (m-40) REVERT: a 390 ASN cc_start: 0.8605 (t0) cc_final: 0.8237 (t0) REVERT: O 22 LYS cc_start: 0.7962 (mttt) cc_final: 0.7738 (mttt) outliers start: 58 outliers final: 51 residues processed: 574 average time/residue: 0.1645 time to fit residues: 157.5323 Evaluate side-chains 601 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 320 SER Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 322 GLN Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 270 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 576 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 449 optimal weight: 0.5980 chunk 475 optimal weight: 5.9990 chunk 483 optimal weight: 0.9980 chunk 314 optimal weight: 0.7980 chunk 573 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN P 322 GLN T 324 ASN ** Y 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093503 restraints weight = 53458.569| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.63 r_work: 0.2779 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 47066 Z= 0.116 Angle : 0.465 9.103 63704 Z= 0.247 Chirality : 0.042 0.174 7251 Planarity : 0.003 0.062 8400 Dihedral : 3.562 21.226 6853 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.19 % Allowed : 12.03 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.11), residues: 6048 helix: 3.08 (0.10), residues: 2576 sheet: 0.87 (0.13), residues: 1526 loop : 0.01 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 26 TYR 0.009 0.001 TYR b 359 PHE 0.031 0.002 PHE I 71 TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS S 365 Details of bonding type rmsd covalent geometry : bond 0.00273 (47066) covalent geometry : angle 0.46463 (63704) hydrogen bonds : bond 0.03389 ( 3023) hydrogen bonds : angle 3.86171 ( 8631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9566.21 seconds wall clock time: 164 minutes 2.38 seconds (9842.38 seconds total)