Starting phenix.real_space_refine on Sun Feb 8 11:21:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.map" model { file = "/net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6w_27224/02_2026/8d6w_27224.cif" } resolution = 3.0 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= 0.004 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 63 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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: 11.43, per 1000 atoms: 0.25 Number of scatterers: 46380 At special positions: 0 Unit cell: (134.964, 133.308, 170.568, 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: 4.74 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: 203 helices and 70 sheets defined 46.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 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 removed outlier: 3.517A pdb=" N VAL A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.557A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.438A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.688A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.595A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.572A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 4.511A 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 113 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.331A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.535A 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: 4.392A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 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 removed outlier: 3.507A pdb=" N VAL F 94 " --> pdb=" O ARG F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.546A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.297A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.699A pdb=" N GLN F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.519A pdb=" N LEU G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.493A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 removed outlier: 3.533A pdb=" N ALA G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.585A pdb=" N GLN G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 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 removed outlier: 3.545A pdb=" N LEU H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.783A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 removed outlier: 3.942A pdb=" N ALA H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) 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 removed outlier: 3.539A pdb=" N PHE I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.690A pdb=" N VAL I 94 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.839A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.859A 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: 3.539A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.270A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 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: 3.678A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.492A 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 226 through 234 removed outlier: 3.528A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) 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: 3.506A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 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: 3.579A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.473A 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 226 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 95 through 114 removed outlier: 3.547A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.391A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) 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 395 removed outlier: 4.799A pdb=" N ALA P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.776A 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: 3.545A 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 389 Processing helix chain 'Q' and resid 390 through 395 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.588A 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: 3.583A 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 395 removed outlier: 4.686A pdb=" N ALA R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.620A 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: 3.635A 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 389 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: 3.724A 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: 3.588A 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 397 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.654A 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: 3.576A 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 396 removed outlier: 3.895A pdb=" N GLN U 396 " --> pdb=" O ALA U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.928A 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: 3.594A 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 Processing helix chain 'V' and resid 390 through 397 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.655A 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: 3.656A 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 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: 3.523A 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: 3.655A 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 395 removed outlier: 4.666A pdb=" N ALA X 392 " --> pdb=" O ARG X 388 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA X 393 " --> pdb=" O GLY X 389 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.815A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.655A 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 397 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.902A 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 521 removed outlier: 3.558A 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 389 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: 3.685A 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: 3.657A 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 389 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.671A 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: 3.545A 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 389 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.720A 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: 3.578A 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 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.693A 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: 3.625A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.508A pdb=" N ARG O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 removed outlier: 3.590A pdb=" N VAL O 94 " --> pdb=" O ARG O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.549A 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: 6.487A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (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: 6.452A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.852A 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 removed outlier: 4.465A pdb=" N VAL D 210 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.464A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.836A 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: 6.511A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.643A pdb=" N VAL F 210 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.507A 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: 6.453A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.896A 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: 6.475A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (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: 6.406A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.690A 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: 6.519A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.868A 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 removed outlier: 4.314A pdb=" N VAL K 210 " --> pdb=" O ILE K 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.496A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.701A 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 removed outlier: 4.371A pdb=" N VAL L 210 " --> pdb=" O ILE L 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.509A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.733A 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: 4.117A 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: 6.421A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.840A 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 removed outlier: 4.357A pdb=" N VAL N 210 " --> pdb=" O ILE N 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.510A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.908A 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: 6.415A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.585A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.866A 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: 6.431A pdb=" N GLN Q 322 " --> pdb=" O ILE Q 326 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE Q 326 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.561A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE Q 420 " --> pdb=" O GLU Q 432 " (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: 6.477A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.633A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (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: 6.306A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET S 325 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.539A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE S 420 " --> pdb=" O GLU S 432 " (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: 6.400A 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: 6.551A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.815A 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: 6.448A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.596A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.775A 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: 6.375A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.587A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.849A 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: 6.377A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.551A 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: 6.470A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.786A 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: 6.496A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 5.875A 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 338 removed outlier: 6.504A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.969A 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: 6.485A 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: 6.562A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.668A 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: 6.463A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.745A 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 336 removed outlier: 3.790A 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: 6.302A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET a 325 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.463A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.946A 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: 6.397A 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: 6.532A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.823A 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: 6.456A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.583A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.734A 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 removed outlier: 4.233A pdb=" N VAL O 210 " --> pdb=" O ILE O 225 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.484A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3042 hydrogen bonds defined for protein. 8718 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: 13.62 Time building geometry restraints manager: 6.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15718 1.34 - 1.46: 7775 1.46 - 1.58: 23362 1.58 - 1.70: 1 1.70 - 1.82: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N VAL Y 439 " pdb=" CA VAL Y 439 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.18e+01 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE R 420 " pdb=" CA ILE R 420 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.80e+00 bond pdb=" N VAL H 155 " pdb=" CA VAL H 155 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.76e+00 bond pdb=" N ILE c 431 " pdb=" CA ILE c 431 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.58e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 62437 1.85 - 3.70: 1126 3.70 - 5.55: 117 5.55 - 7.40: 19 7.40 - 9.24: 5 Bond angle restraints: 63704 Sorted by residual: angle pdb=" O TYR D 89 " pdb=" C TYR D 89 " pdb=" N ASP D 90 " ideal model delta sigma weight residual 120.83 124.17 -3.34 7.40e-01 1.83e+00 2.03e+01 angle pdb=" CA PRO D 151 " pdb=" N PRO D 151 " pdb=" CD PRO D 151 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" CA GLY H 157 " pdb=" C GLY H 157 " pdb=" O GLY H 157 " ideal model delta sigma weight residual 122.39 118.48 3.91 9.30e-01 1.16e+00 1.76e+01 angle pdb=" CA GLY b 418 " pdb=" C GLY b 418 " pdb=" O GLY b 418 " ideal model delta sigma weight residual 121.41 117.99 3.42 8.80e-01 1.29e+00 1.51e+01 angle pdb=" C GLN E 11 " pdb=" N ALA E 12 " pdb=" CA ALA E 12 " ideal model delta sigma weight residual 120.28 125.82 -5.54 1.44e+00 4.82e-01 1.48e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25314 17.99 - 35.97: 2275 35.97 - 53.96: 595 53.96 - 71.95: 104 71.95 - 89.93: 47 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL A 212 " pdb=" C VAL A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL O 212 " pdb=" C VAL O 212 " pdb=" N LEU O 213 " pdb=" CA LEU O 213 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL J 212 " pdb=" C VAL J 212 " pdb=" N LEU J 213 " pdb=" CA LEU J 213 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5513 0.048 - 0.096: 1299 0.096 - 0.144: 394 0.144 - 0.191: 38 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ALA E 12 " pdb=" N ALA E 12 " pdb=" C ALA E 12 " pdb=" CB ALA E 12 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL D 30 " pdb=" N VAL D 30 " pdb=" C VAL D 30 " pdb=" CB VAL D 30 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE c 420 " pdb=" N ILE c 420 " pdb=" C ILE c 420 " pdb=" CB ILE c 420 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Y 413 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO Y 414 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO Y 414 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO Y 414 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 118 " 0.028 2.00e-02 2.50e+03 2.10e-02 8.82e+00 pdb=" CG TYR I 118 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR I 118 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR I 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 118 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I 118 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR I 118 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 118 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 150 " -0.041 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 151 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3238 2.74 - 3.28: 44324 3.28 - 3.82: 79864 3.82 - 4.36: 94799 4.36 - 4.90: 166365 Nonbonded interactions: 388590 Sorted by model distance: nonbonded pdb=" O ALA A 34 " pdb=" OH TYR A 171 " model vdw 2.197 3.040 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.198 3.040 nonbonded pdb=" O ALA G 166 " pdb=" OG SER G 170 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 142 " pdb=" OD1 ASP A 144 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG R 329 " pdb=" O ASP a 476 " model vdw 2.209 3.120 ... (remaining 388585 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: 8.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 49.360 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.004 0.117 47066 Z= 0.218 Angle : 0.599 9.244 63704 Z= 0.349 Chirality : 0.045 0.239 7251 Planarity : 0.004 0.096 8400 Dihedral : 15.251 89.932 17177 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.53 % Allowed : 13.28 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.61 (0.11), residues: 6048 helix: 2.27 (0.10), residues: 2520 sheet: 0.79 (0.13), residues: 1526 loop : -0.21 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 135 TYR 0.049 0.001 TYR I 118 PHE 0.032 0.002 PHE M 71 TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS X 365 Details of bonding type rmsd covalent geometry : bond 0.00381 (47066) covalent geometry : angle 0.59921 (63704) hydrogen bonds : bond 0.09417 ( 3042) hydrogen bonds : angle 5.06090 ( 8718) *********************** 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 730 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 659 time to evaluate : 1.885 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8122 (mt0) cc_final: 0.7908 (mt0) REVERT: A 90 ASP cc_start: 0.8403 (t70) cc_final: 0.8159 (t70) REVERT: C 80 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7367 (mt0) REVERT: C 118 TYR cc_start: 0.7446 (m-10) cc_final: 0.7167 (m-10) REVERT: C 135 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6532 (mtt90) REVERT: D 134 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6768 (pptt) REVERT: E 80 GLN cc_start: 0.7959 (tp40) cc_final: 0.7745 (mm-40) REVERT: E 137 GLU cc_start: 0.6971 (mp0) cc_final: 0.6747 (pm20) REVERT: F 21 ARG cc_start: 0.6183 (ptp90) cc_final: 0.5843 (ttp-170) REVERT: F 53 ILE cc_start: 0.8437 (mm) cc_final: 0.8173 (mt) REVERT: F 209 GLU cc_start: 0.6787 (tt0) cc_final: 0.6559 (tt0) REVERT: G 26 ARG cc_start: 0.6949 (ptt-90) cc_final: 0.6669 (ptt180) REVERT: G 169 GLU cc_start: 0.6172 (mm-30) cc_final: 0.4988 (tp30) REVERT: H 67 LYS cc_start: 0.7607 (tttt) cc_final: 0.7362 (tttm) REVERT: H 121 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: H 152 HIS cc_start: 0.7231 (m90) cc_final: 0.6462 (m90) REVERT: I 70 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: I 153 PHE cc_start: 0.6840 (p90) cc_final: 0.6383 (p90) REVERT: I 159 THR cc_start: 0.6372 (p) cc_final: 0.5644 (t) REVERT: J 182 ARG cc_start: 0.6043 (mtt90) cc_final: 0.5784 (tpp-160) REVERT: J 214 ASP cc_start: 0.7895 (t0) cc_final: 0.7450 (t70) REVERT: M 13 MET cc_start: 0.7915 (mmm) cc_final: 0.7450 (mmp) REVERT: N 54 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8846 (p) REVERT: N 168 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7153 (tppt) REVERT: R 354 GLU cc_start: 0.7527 (tt0) cc_final: 0.7246 (tt0) REVERT: T 339 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: U 386 MET cc_start: 0.8922 (ttm) cc_final: 0.8692 (ttm) REVERT: V 364 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7587 (mt-10) REVERT: X 325 MET cc_start: 0.8055 (ttp) cc_final: 0.7575 (tpp) REVERT: Y 341 THR cc_start: 0.8949 (p) cc_final: 0.8674 (t) REVERT: Y 500 ASP cc_start: 0.8123 (m-30) cc_final: 0.7843 (m-30) REVERT: Z 324 ASN cc_start: 0.7863 (m-40) cc_final: 0.7504 (p0) REVERT: Z 500 ASP cc_start: 0.8269 (m-30) cc_final: 0.8044 (m-30) REVERT: c 325 MET cc_start: 0.8126 (ttp) cc_final: 0.7897 (tmt) outliers start: 71 outliers final: 23 residues processed: 708 average time/residue: 0.7996 time to fit residues: 697.3275 Evaluate side-chains 558 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 531 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain T residue 339 ASP Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain a residue 416 SER Chi-restraints excluded: chain a residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 8.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 4.9990 chunk 597 optimal weight: 0.8980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 105 GLN C 73 ASN D 11 GLN D 51 GLN E 105 GLN E 165 ASN F 45 ASN F 51 GLN F 101 ASN G 73 ASN H 11 GLN H 80 GLN J 11 GLN J 73 ASN J 165 ASN K 129 HIS K 216 ASN L 105 GLN L 165 ASN M 105 GLN N 45 ASN N 80 GLN P 322 GLN Q 390 ASN S 324 ASN T 437 GLN U 365 HIS U 437 GLN V 437 GLN X 322 GLN X 456 GLN Y 437 GLN b 324 ASN b 390 ASN c 322 GLN c 396 GLN d 172 GLN O 152 HIS O 231 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.090393 restraints weight = 56968.777| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.65 r_work: 0.2860 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 47066 Z= 0.164 Angle : 0.533 8.726 63704 Z= 0.286 Chirality : 0.044 0.177 7251 Planarity : 0.004 0.063 8400 Dihedral : 4.743 104.212 6894 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.08 % Allowed : 14.74 % Favored : 82.18 % 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: 1.82 (0.11), residues: 6048 helix: 2.46 (0.10), residues: 2548 sheet: 0.85 (0.13), residues: 1526 loop : -0.14 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 14 TYR 0.016 0.001 TYR J 171 PHE 0.038 0.003 PHE C 71 TRP 0.006 0.001 TRP Z 429 HIS 0.006 0.001 HIS Q 365 Details of bonding type rmsd covalent geometry : bond 0.00369 (47066) covalent geometry : angle 0.53314 (63704) hydrogen bonds : bond 0.03695 ( 3042) hydrogen bonds : angle 4.29558 ( 8718) *********************** 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 737 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 594 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7124 (mp0) REVERT: C 80 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7687 (mt0) REVERT: D 13 MET cc_start: 0.4945 (tmm) cc_final: 0.4552 (tpp) REVERT: D 113 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6154 (mp0) REVERT: D 203 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5288 (tp) REVERT: E 13 MET cc_start: 0.6173 (mmm) cc_final: 0.4960 (mmp) REVERT: E 80 GLN cc_start: 0.8467 (tp40) cc_final: 0.8137 (tp-100) REVERT: E 113 GLU cc_start: 0.6070 (tt0) cc_final: 0.5563 (mt-10) REVERT: E 114 GLN cc_start: 0.5941 (OUTLIER) cc_final: 0.5614 (mm110) REVERT: E 121 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: E 135 ARG cc_start: 0.7352 (ptm160) cc_final: 0.7017 (ptm160) REVERT: E 165 ASN cc_start: 0.5856 (m-40) cc_final: 0.5498 (m-40) REVERT: F 21 ARG cc_start: 0.6484 (ptp90) cc_final: 0.6062 (ttp-170) REVERT: F 29 SER cc_start: 0.6900 (m) cc_final: 0.6536 (p) REVERT: F 70 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: F 116 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5327 (tmmt) REVERT: G 21 ARG cc_start: 0.7346 (tpt-90) cc_final: 0.7113 (ttp80) REVERT: G 97 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: G 176 SER cc_start: 0.7499 (m) cc_final: 0.7003 (p) REVERT: H 13 MET cc_start: 0.6360 (tpp) cc_final: 0.6025 (tpt) REVERT: H 33 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7475 (pp) REVERT: H 152 HIS cc_start: 0.7440 (m90) cc_final: 0.6407 (m-70) REVERT: I 70 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: I 153 PHE cc_start: 0.7048 (p90) cc_final: 0.6354 (p90) REVERT: J 182 ARG cc_start: 0.6267 (mtt90) cc_final: 0.5997 (tpp-160) REVERT: K 168 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7418 (mttt) REVERT: K 203 LEU cc_start: 0.6691 (mp) cc_final: 0.5806 (mt) REVERT: M 80 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: M 143 TYR cc_start: 0.8840 (p90) cc_final: 0.8536 (p90) REVERT: M 149 ASP cc_start: 0.7855 (t0) cc_final: 0.7596 (t0) REVERT: N 14 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6669 (ttp80) REVERT: N 21 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7233 (ttm-80) REVERT: N 168 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7255 (tptp) REVERT: P 339 ASP cc_start: 0.8291 (t0) cc_final: 0.7933 (t0) REVERT: S 361 VAL cc_start: 0.8946 (t) cc_final: 0.8694 (t) REVERT: T 339 ASP cc_start: 0.8395 (m-30) cc_final: 0.8164 (m-30) REVERT: U 395 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6596 (mpt) REVERT: V 401 LEU cc_start: 0.8677 (mm) cc_final: 0.8474 (mp) REVERT: X 325 MET cc_start: 0.8444 (ttp) cc_final: 0.7935 (tpp) REVERT: X 512 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: Y 398 LEU cc_start: 0.7991 (mt) cc_final: 0.7758 (mt) REVERT: Z 500 ASP cc_start: 0.8699 (m-30) cc_final: 0.8491 (m-30) REVERT: a 325 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7827 (tmm) REVERT: O 15 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6649 (mt-10) outliers start: 143 outliers final: 41 residues processed: 672 average time/residue: 0.7836 time to fit residues: 647.9174 Evaluate side-chains 580 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 526 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 153 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 339 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 321 THR Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 325 MET Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 422 SER Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 509 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 486 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 517 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN H 80 GLN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN R 390 ASN S 324 ASN S 390 ASN U 381 ASN X 322 GLN b 390 ASN c 322 GLN h 172 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.088442 restraints weight = 56910.372| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.65 r_work: 0.2831 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 47066 Z= 0.196 Angle : 0.546 7.702 63704 Z= 0.290 Chirality : 0.044 0.184 7251 Planarity : 0.004 0.056 8400 Dihedral : 4.518 104.802 6862 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 15.73 % Favored : 80.62 % 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: 1.83 (0.11), residues: 6048 helix: 2.51 (0.10), residues: 2548 sheet: 0.82 (0.13), residues: 1526 loop : -0.15 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 14 TYR 0.014 0.001 TYR J 171 PHE 0.036 0.003 PHE M 71 TRP 0.008 0.001 TRP c 429 HIS 0.005 0.001 HIS X 365 Details of bonding type rmsd covalent geometry : bond 0.00466 (47066) covalent geometry : angle 0.54602 (63704) hydrogen bonds : bond 0.04127 ( 3042) hydrogen bonds : angle 4.36636 ( 8718) *********************** 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 704 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 535 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: A 161 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7240 (mp0) REVERT: C 132 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: D 13 MET cc_start: 0.5067 (tmm) cc_final: 0.4695 (tpp) REVERT: D 134 LYS cc_start: 0.7275 (tmtt) cc_final: 0.6802 (pptt) REVERT: D 135 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6571 (ttp80) REVERT: D 203 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5352 (tp) REVERT: E 13 MET cc_start: 0.6313 (mmm) cc_final: 0.5043 (mmp) REVERT: E 80 GLN cc_start: 0.8543 (tp40) cc_final: 0.8212 (tp-100) REVERT: E 112 THR cc_start: 0.7096 (m) cc_final: 0.6738 (t) REVERT: E 113 GLU cc_start: 0.5962 (tt0) cc_final: 0.5397 (mt-10) REVERT: E 165 ASN cc_start: 0.5773 (m-40) cc_final: 0.5465 (m-40) REVERT: F 29 SER cc_start: 0.6912 (m) cc_final: 0.6565 (p) REVERT: F 70 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: F 80 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: F 116 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.4733 (tmmt) REVERT: G 21 ARG cc_start: 0.7297 (tpt-90) cc_final: 0.7091 (ttp80) REVERT: G 97 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: G 176 SER cc_start: 0.7576 (m) cc_final: 0.6955 (p) REVERT: H 156 MET cc_start: 0.7849 (mtm) cc_final: 0.7608 (mtm) REVERT: I 159 THR cc_start: 0.6281 (OUTLIER) cc_final: 0.5585 (t) REVERT: J 182 ARG cc_start: 0.6251 (mtt90) cc_final: 0.6006 (tpp-160) REVERT: K 203 LEU cc_start: 0.6669 (mp) cc_final: 0.5806 (mt) REVERT: M 80 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: M 105 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8265 (mp-120) REVERT: M 143 TYR cc_start: 0.8892 (p90) cc_final: 0.8633 (p90) REVERT: M 149 ASP cc_start: 0.7840 (t0) cc_final: 0.7563 (t0) REVERT: N 14 ARG cc_start: 0.7087 (ttp-110) cc_final: 0.6799 (ttp80) REVERT: N 21 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7293 (ttm-80) REVERT: N 168 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7238 (tptp) REVERT: P 330 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8165 (p0) REVERT: S 361 VAL cc_start: 0.9067 (t) cc_final: 0.8769 (t) REVERT: T 339 ASP cc_start: 0.8369 (m-30) cc_final: 0.8154 (m-30) REVERT: T 430 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7718 (m110) REVERT: U 395 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6718 (mpt) REVERT: U 401 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8260 (tt) REVERT: U 430 ASN cc_start: 0.8543 (t0) cc_final: 0.8254 (t0) REVERT: V 401 LEU cc_start: 0.8693 (mm) cc_final: 0.8489 (mp) REVERT: W 325 MET cc_start: 0.8136 (tmt) cc_final: 0.7837 (tmm) REVERT: W 509 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7296 (ttp-170) REVERT: X 512 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: Y 398 LEU cc_start: 0.8265 (mt) cc_final: 0.8057 (mt) REVERT: Z 398 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7897 (mt) REVERT: Z 447 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8495 (mtmp) REVERT: O 15 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6449 (mt-10) REVERT: O 51 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7900 (mm-40) outliers start: 169 outliers final: 64 residues processed: 635 average time/residue: 0.7907 time to fit residues: 617.5754 Evaluate side-chains 593 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 508 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 358 LEU Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 414 optimal weight: 10.0000 chunk 470 optimal weight: 0.6980 chunk 407 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 555 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 389 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN H 80 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN N 45 ASN N 80 GLN P 322 GLN P 390 ASN S 324 ASN b 390 ASN c 322 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.092518 restraints weight = 56242.439| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.67 r_work: 0.2785 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 47066 Z= 0.133 Angle : 0.492 7.150 63704 Z= 0.263 Chirality : 0.043 0.199 7251 Planarity : 0.004 0.050 8400 Dihedral : 4.141 72.517 6859 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.04 % Allowed : 16.85 % Favored : 80.11 % 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: 2.01 (0.11), residues: 6048 helix: 2.71 (0.10), residues: 2548 sheet: 0.85 (0.13), residues: 1526 loop : -0.09 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 14 TYR 0.013 0.001 TYR C 143 PHE 0.032 0.002 PHE M 71 TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS X 365 Details of bonding type rmsd covalent geometry : bond 0.00305 (47066) covalent geometry : angle 0.49159 (63704) hydrogen bonds : bond 0.03534 ( 3042) hydrogen bonds : angle 4.24604 ( 8718) *********************** 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 695 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 554 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7234 (mp0) REVERT: C 132 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6366 (mt-10) REVERT: D 13 MET cc_start: 0.4999 (tmm) cc_final: 0.4631 (tpp) REVERT: D 135 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6521 (ttp80) REVERT: D 203 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5316 (tp) REVERT: E 13 MET cc_start: 0.6039 (mmm) cc_final: 0.4842 (mmp) REVERT: E 80 GLN cc_start: 0.8556 (tp40) cc_final: 0.8229 (tp-100) REVERT: E 112 THR cc_start: 0.6960 (m) cc_final: 0.6621 (t) REVERT: E 121 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: E 135 ARG cc_start: 0.7372 (ptm160) cc_final: 0.7040 (ptm160) REVERT: E 165 ASN cc_start: 0.5757 (m-40) cc_final: 0.5448 (m-40) REVERT: F 29 SER cc_start: 0.6944 (m) cc_final: 0.6599 (p) REVERT: F 70 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: F 80 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: F 116 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.4671 (tmmt) REVERT: G 21 ARG cc_start: 0.7287 (tpt-90) cc_final: 0.7059 (ttp80) REVERT: G 97 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7313 (ttm170) REVERT: G 176 SER cc_start: 0.7561 (m) cc_final: 0.6932 (p) REVERT: H 33 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7446 (pp) REVERT: I 13 MET cc_start: 0.6591 (mmm) cc_final: 0.6280 (mmt) REVERT: I 159 THR cc_start: 0.6199 (p) cc_final: 0.5520 (t) REVERT: K 168 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7318 (mttt) REVERT: K 203 LEU cc_start: 0.6635 (mp) cc_final: 0.5749 (mt) REVERT: M 105 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8167 (mp-120) REVERT: M 143 TYR cc_start: 0.8849 (p90) cc_final: 0.8557 (p90) REVERT: M 149 ASP cc_start: 0.7817 (t0) cc_final: 0.7526 (t0) REVERT: N 14 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6730 (ttp80) REVERT: N 21 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7262 (ttm-80) REVERT: N 24 ILE cc_start: 0.8181 (mm) cc_final: 0.7917 (mt) REVERT: R 325 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8068 (ttt) REVERT: S 361 VAL cc_start: 0.8985 (t) cc_final: 0.8719 (t) REVERT: T 339 ASP cc_start: 0.8417 (m-30) cc_final: 0.8207 (m-30) REVERT: T 430 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (m110) REVERT: T 509 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6622 (tpt-90) REVERT: U 395 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6707 (mpt) REVERT: U 430 ASN cc_start: 0.8519 (t0) cc_final: 0.8207 (t0) REVERT: W 325 MET cc_start: 0.8162 (tmt) cc_final: 0.7849 (tmm) REVERT: W 509 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7148 (ttp-110) REVERT: X 512 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: Y 398 LEU cc_start: 0.8172 (mt) cc_final: 0.7962 (mt) REVERT: Z 398 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7844 (mt) REVERT: O 15 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6423 (mt-10) outliers start: 141 outliers final: 63 residues processed: 641 average time/residue: 0.5746 time to fit residues: 458.2092 Evaluate side-chains 606 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 525 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 292 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 414 optimal weight: 0.0070 chunk 561 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 372 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 chunk 423 optimal weight: 9.9990 chunk 389 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 80 GLN J 165 ASN K 216 ASN L 101 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 390 ASN S 324 ASN U 381 ASN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.090020 restraints weight = 56602.973| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.65 r_work: 0.2789 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 47066 Z= 0.125 Angle : 0.480 7.203 63704 Z= 0.257 Chirality : 0.042 0.171 7251 Planarity : 0.004 0.047 8400 Dihedral : 4.026 69.338 6859 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.89 % Allowed : 17.52 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.11), residues: 6048 helix: 2.83 (0.10), residues: 2548 sheet: 0.88 (0.14), residues: 1526 loop : -0.07 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 14 TYR 0.015 0.001 TYR C 143 PHE 0.032 0.002 PHE M 71 TRP 0.004 0.001 TRP c 429 HIS 0.004 0.001 HIS Q 365 Details of bonding type rmsd covalent geometry : bond 0.00287 (47066) covalent geometry : angle 0.48031 (63704) hydrogen bonds : bond 0.03388 ( 3042) hydrogen bonds : angle 4.18027 ( 8718) *********************** 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 683 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 549 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7243 (mp0) REVERT: C 132 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6377 (mt-10) REVERT: D 13 MET cc_start: 0.4905 (tmm) cc_final: 0.4590 (tpp) REVERT: E 13 MET cc_start: 0.5989 (mmm) cc_final: 0.4797 (mmp) REVERT: E 80 GLN cc_start: 0.8565 (tp40) cc_final: 0.8238 (tp-100) REVERT: E 112 THR cc_start: 0.6992 (m) cc_final: 0.6737 (t) REVERT: E 114 GLN cc_start: 0.5865 (OUTLIER) cc_final: 0.5375 (mm110) REVERT: E 121 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: E 135 ARG cc_start: 0.7352 (ptm160) cc_final: 0.7048 (ptm160) REVERT: E 165 ASN cc_start: 0.5736 (m-40) cc_final: 0.5433 (m-40) REVERT: E 230 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6542 (tt) REVERT: F 29 SER cc_start: 0.6914 (m) cc_final: 0.6526 (p) REVERT: F 70 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: F 80 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: F 116 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.4646 (tmmt) REVERT: F 234 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6258 (pp) REVERT: G 97 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7306 (ttm170) REVERT: G 176 SER cc_start: 0.7541 (m) cc_final: 0.6905 (p) REVERT: H 33 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7433 (pp) REVERT: I 13 MET cc_start: 0.6456 (mmm) cc_final: 0.6126 (mmt) REVERT: I 70 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: I 159 THR cc_start: 0.6164 (p) cc_final: 0.5475 (t) REVERT: K 48 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6835 (mmp-170) REVERT: K 168 LYS cc_start: 0.7981 (mtpp) cc_final: 0.7339 (mttt) REVERT: K 203 LEU cc_start: 0.6520 (mp) cc_final: 0.5706 (mt) REVERT: M 105 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8112 (mp-120) REVERT: M 143 TYR cc_start: 0.8837 (p90) cc_final: 0.8538 (p90) REVERT: M 149 ASP cc_start: 0.7815 (t0) cc_final: 0.7549 (t0) REVERT: N 13 MET cc_start: 0.7632 (tpp) cc_final: 0.6577 (mpp) REVERT: N 14 ARG cc_start: 0.7145 (ttp-110) cc_final: 0.6806 (ttp80) REVERT: N 21 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7283 (ttm-80) REVERT: N 24 ILE cc_start: 0.8136 (mm) cc_final: 0.7876 (mt) REVERT: P 330 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (p0) REVERT: Q 339 ASP cc_start: 0.8337 (m-30) cc_final: 0.8047 (t70) REVERT: Q 519 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7701 (mp0) REVERT: R 325 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8050 (ttt) REVERT: S 361 VAL cc_start: 0.8978 (t) cc_final: 0.8717 (t) REVERT: T 339 ASP cc_start: 0.8433 (m-30) cc_final: 0.8216 (m-30) REVERT: T 430 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7754 (m110) REVERT: T 509 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6626 (tpt-90) REVERT: U 395 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6714 (mpt) REVERT: U 430 ASN cc_start: 0.8496 (t0) cc_final: 0.8197 (t0) REVERT: W 325 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: W 430 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8050 (t0) REVERT: W 509 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7145 (ttp-110) REVERT: X 512 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: Z 398 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7886 (mt) REVERT: O 15 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: O 51 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7891 (mm-40) REVERT: O 219 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8209 (ttp80) outliers start: 134 outliers final: 65 residues processed: 633 average time/residue: 0.4979 time to fit residues: 391.9033 Evaluate side-chains 611 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 521 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 447 LYS Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 596 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 589 optimal weight: 7.9990 chunk 393 optimal weight: 1.9990 chunk 337 optimal weight: 6.9990 chunk 487 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 375 optimal weight: 0.9980 chunk 467 optimal weight: 7.9990 chunk 61 optimal weight: 0.0170 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 45 ASN H 80 GLN K 216 ASN L 165 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 ASN N 80 GLN P 322 GLN P 390 ASN P 437 GLN S 324 ASN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.091533 restraints weight = 56711.757| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.64 r_work: 0.2890 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 47066 Z= 0.103 Angle : 0.460 7.743 63704 Z= 0.247 Chirality : 0.042 0.165 7251 Planarity : 0.003 0.046 8400 Dihedral : 3.870 65.555 6857 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.56 % Allowed : 18.60 % Favored : 78.84 % 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: 2534 sheet: 0.90 (0.14), residues: 1526 loop : 0.02 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 14 TYR 0.015 0.001 TYR C 143 PHE 0.031 0.002 PHE M 71 TRP 0.003 0.001 TRP c 429 HIS 0.004 0.001 HIS X 365 Details of bonding type rmsd covalent geometry : bond 0.00227 (47066) covalent geometry : angle 0.45963 (63704) hydrogen bonds : bond 0.03112 ( 3042) hydrogen bonds : angle 4.09086 ( 8718) *********************** 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 677 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 558 time to evaluate : 1.771 Fit side-chains REVERT: A 161 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7309 (mp0) REVERT: C 13 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5317 (mmt) REVERT: C 132 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6425 (mt-10) REVERT: D 13 MET cc_start: 0.4810 (tmm) cc_final: 0.4467 (tpp) REVERT: E 13 MET cc_start: 0.5964 (mmm) cc_final: 0.4831 (mmp) REVERT: E 80 GLN cc_start: 0.8541 (tp40) cc_final: 0.8223 (tp-100) REVERT: E 112 THR cc_start: 0.7021 (m) cc_final: 0.6803 (t) REVERT: E 114 GLN cc_start: 0.5860 (OUTLIER) cc_final: 0.5394 (mm110) REVERT: E 121 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: E 165 ASN cc_start: 0.5637 (m-40) cc_final: 0.5394 (m-40) REVERT: F 29 SER cc_start: 0.6903 (m) cc_final: 0.6522 (p) REVERT: F 80 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: F 116 LYS cc_start: 0.6024 (OUTLIER) cc_final: 0.4674 (tmmt) REVERT: G 97 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7299 (ttm170) REVERT: G 119 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: G 176 SER cc_start: 0.7439 (m) cc_final: 0.6953 (p) REVERT: H 33 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7471 (pp) REVERT: H 152 HIS cc_start: 0.7536 (m90) cc_final: 0.6700 (m90) REVERT: I 13 MET cc_start: 0.6466 (mmm) cc_final: 0.6126 (mmt) REVERT: I 159 THR cc_start: 0.6199 (OUTLIER) cc_final: 0.5432 (t) REVERT: K 48 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7001 (mmp-170) REVERT: K 203 LEU cc_start: 0.6496 (mp) cc_final: 0.5682 (mt) REVERT: M 105 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8300 (mm110) REVERT: M 143 TYR cc_start: 0.8831 (p90) cc_final: 0.8575 (p90) REVERT: M 149 ASP cc_start: 0.7759 (t0) cc_final: 0.7491 (t0) REVERT: N 13 MET cc_start: 0.7643 (tpp) cc_final: 0.6577 (mpp) REVERT: N 14 ARG cc_start: 0.7147 (ttp-110) cc_final: 0.6812 (ttp80) REVERT: N 21 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7406 (ttm-80) REVERT: P 330 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (p0) REVERT: Q 339 ASP cc_start: 0.8302 (m-30) cc_final: 0.8018 (t70) REVERT: Q 519 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7706 (mp0) REVERT: R 339 ASP cc_start: 0.8702 (t0) cc_final: 0.8397 (t0) REVERT: S 361 VAL cc_start: 0.8959 (t) cc_final: 0.8707 (t) REVERT: S 509 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7266 (ttt180) REVERT: T 339 ASP cc_start: 0.8384 (m-30) cc_final: 0.8175 (m-30) REVERT: T 430 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7675 (m110) REVERT: T 509 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6620 (tpt-90) REVERT: U 395 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6687 (mpt) REVERT: U 401 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (tt) REVERT: U 430 ASN cc_start: 0.8498 (t0) cc_final: 0.8238 (t0) REVERT: W 325 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: W 430 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8073 (t0) REVERT: W 509 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7154 (ttp-170) REVERT: X 512 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: Y 395 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6187 (mpt) REVERT: Z 398 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7901 (mt) REVERT: b 325 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: b 354 GLU cc_start: 0.8133 (tt0) cc_final: 0.7426 (pt0) REVERT: O 15 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6522 (mt-10) outliers start: 119 outliers final: 56 residues processed: 630 average time/residue: 0.4966 time to fit residues: 388.6320 Evaluate side-chains 605 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 523 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 390 optimal weight: 0.6980 chunk 258 optimal weight: 0.8980 chunk 379 optimal weight: 0.0980 chunk 476 optimal weight: 7.9990 chunk 485 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 439 optimal weight: 0.7980 chunk 579 optimal weight: 0.9990 chunk 136 optimal weight: 0.0370 chunk 207 optimal weight: 7.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 45 ASN H 80 GLN J 11 GLN J 165 ASN K 216 ASN L 105 GLN L 165 ASN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN U 381 ASN Z 322 GLN b 390 ASN c 322 GLN d 172 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.093367 restraints weight = 56370.183| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.64 r_work: 0.2913 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 47066 Z= 0.089 Angle : 0.450 8.008 63704 Z= 0.241 Chirality : 0.041 0.184 7251 Planarity : 0.003 0.045 8400 Dihedral : 3.697 59.993 6857 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 19.01 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.44 (0.11), residues: 6048 helix: 3.21 (0.10), residues: 2534 sheet: 0.93 (0.14), residues: 1526 loop : 0.07 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG H 21 TYR 0.013 0.001 TYR C 171 PHE 0.030 0.002 PHE C 71 TRP 0.003 0.001 TRP T 429 HIS 0.004 0.001 HIS Q 365 Details of bonding type rmsd covalent geometry : bond 0.00191 (47066) covalent geometry : angle 0.45010 (63704) hydrogen bonds : bond 0.02834 ( 3042) hydrogen bonds : angle 3.99234 ( 8718) *********************** 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 689 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 585 time to evaluate : 1.082 Fit side-chains REVERT: A 161 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7262 (mp0) REVERT: C 13 MET cc_start: 0.5725 (mpp) cc_final: 0.5465 (mmt) REVERT: C 132 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: D 13 MET cc_start: 0.4733 (tmm) cc_final: 0.4490 (tpp) REVERT: E 13 MET cc_start: 0.5900 (mmm) cc_final: 0.4848 (mmt) REVERT: E 45 ASN cc_start: 0.6656 (t0) cc_final: 0.6357 (t160) REVERT: E 80 GLN cc_start: 0.8520 (tp40) cc_final: 0.8184 (tp-100) REVERT: E 121 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: E 135 ARG cc_start: 0.7340 (ptm160) cc_final: 0.7064 (ptm160) REVERT: E 165 ASN cc_start: 0.5788 (m-40) cc_final: 0.5534 (m-40) REVERT: E 219 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8025 (ttp-110) REVERT: F 29 SER cc_start: 0.6957 (m) cc_final: 0.6749 (t) REVERT: F 116 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.4609 (tmmt) REVERT: G 97 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7277 (ttm170) REVERT: G 119 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: G 169 GLU cc_start: 0.6653 (mm-30) cc_final: 0.5305 (tp30) REVERT: G 176 SER cc_start: 0.7360 (m) cc_final: 0.6872 (p) REVERT: H 33 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7447 (pp) REVERT: H 152 HIS cc_start: 0.7483 (m90) cc_final: 0.6705 (m90) REVERT: I 13 MET cc_start: 0.6434 (mmm) cc_final: 0.6099 (mmt) REVERT: I 159 THR cc_start: 0.6186 (p) cc_final: 0.5809 (p) REVERT: K 48 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6978 (mmp-170) REVERT: K 168 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7370 (mttt) REVERT: K 203 LEU cc_start: 0.6405 (mp) cc_final: 0.5634 (mt) REVERT: M 143 TYR cc_start: 0.8794 (p90) cc_final: 0.8525 (p90) REVERT: M 149 ASP cc_start: 0.7748 (t0) cc_final: 0.7473 (t0) REVERT: N 13 MET cc_start: 0.7625 (tpp) cc_final: 0.6541 (mpp) REVERT: N 14 ARG cc_start: 0.7145 (ttp-110) cc_final: 0.6797 (ttp80) REVERT: N 176 SER cc_start: 0.8076 (t) cc_final: 0.7660 (p) REVERT: P 330 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8013 (p0) REVERT: Q 339 ASP cc_start: 0.8270 (m-30) cc_final: 0.7985 (t70) REVERT: R 339 ASP cc_start: 0.8703 (t0) cc_final: 0.8411 (t0) REVERT: S 361 VAL cc_start: 0.8940 (t) cc_final: 0.8691 (t) REVERT: S 509 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7200 (ttt180) REVERT: T 339 ASP cc_start: 0.8380 (m-30) cc_final: 0.8054 (m-30) REVERT: T 509 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6591 (tpt-90) REVERT: U 395 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6673 (mpt) REVERT: U 430 ASN cc_start: 0.8481 (t0) cc_final: 0.8223 (t0) REVERT: W 325 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7862 (tmm) REVERT: W 430 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8076 (t0) REVERT: W 509 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7155 (ttp-110) REVERT: Y 395 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6165 (mpt) REVERT: Z 398 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7922 (mt) REVERT: Z 424 ASP cc_start: 0.8007 (p0) cc_final: 0.7778 (p0) REVERT: Z 432 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: a 339 ASP cc_start: 0.8173 (p0) cc_final: 0.7857 (t70) REVERT: b 354 GLU cc_start: 0.8078 (tt0) cc_final: 0.7396 (pt0) REVERT: O 15 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: O 219 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8173 (ttp80) outliers start: 104 outliers final: 49 residues processed: 646 average time/residue: 0.4879 time to fit residues: 391.8940 Evaluate side-chains 602 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 535 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 28 optimal weight: 2.9990 chunk 588 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 524 optimal weight: 8.9990 chunk 492 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 568 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN G 73 ASN H 45 ASN H 80 GLN K 216 ASN L 105 GLN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN R 415 GLN U 381 ASN X 396 GLN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.090245 restraints weight = 56648.180| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.66 r_work: 0.2854 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 47066 Z= 0.140 Angle : 0.497 9.688 63704 Z= 0.263 Chirality : 0.043 0.176 7251 Planarity : 0.004 0.051 8400 Dihedral : 3.862 56.346 6856 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.54 % Allowed : 18.94 % Favored : 78.51 % 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: 2.30 (0.11), residues: 6048 helix: 2.98 (0.10), residues: 2562 sheet: 0.95 (0.14), residues: 1526 loop : 0.03 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 135 TYR 0.014 0.001 TYR N 118 PHE 0.032 0.002 PHE M 71 TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 Details of bonding type rmsd covalent geometry : bond 0.00326 (47066) covalent geometry : angle 0.49732 (63704) hydrogen bonds : bond 0.03369 ( 3042) hydrogen bonds : angle 4.07940 ( 8718) *********************** 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 660 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 542 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: A 161 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7280 (mp0) REVERT: C 13 MET cc_start: 0.5837 (OUTLIER) cc_final: 0.5406 (mmt) REVERT: C 132 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6456 (mt-10) REVERT: D 13 MET cc_start: 0.4741 (tmm) cc_final: 0.4540 (tpp) REVERT: D 21 ARG cc_start: 0.6582 (mtt90) cc_final: 0.6335 (mmt-90) REVERT: E 13 MET cc_start: 0.5897 (mmm) cc_final: 0.4818 (mmp) REVERT: E 22 LYS cc_start: 0.7460 (mtpt) cc_final: 0.6768 (ptpp) REVERT: E 45 ASN cc_start: 0.6752 (t0) cc_final: 0.6433 (t160) REVERT: E 80 GLN cc_start: 0.8533 (tp40) cc_final: 0.8182 (tp-100) REVERT: E 165 ASN cc_start: 0.5682 (m-40) cc_final: 0.5440 (m110) REVERT: E 219 ARG cc_start: 0.8572 (tmm-80) cc_final: 0.8157 (ttp-110) REVERT: F 80 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: F 116 LYS cc_start: 0.5931 (OUTLIER) cc_final: 0.4964 (tmmt) REVERT: F 168 LYS cc_start: 0.6316 (mmmm) cc_final: 0.5986 (mtmt) REVERT: F 234 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6095 (pp) REVERT: G 97 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7313 (ttm170) REVERT: G 119 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: G 176 SER cc_start: 0.7392 (m) cc_final: 0.6932 (p) REVERT: G 233 LEU cc_start: 0.7224 (mp) cc_final: 0.6886 (tp) REVERT: H 33 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7450 (pp) REVERT: H 152 HIS cc_start: 0.7439 (m90) cc_final: 0.6597 (m90) REVERT: I 13 MET cc_start: 0.6432 (mmm) cc_final: 0.6109 (mmt) REVERT: I 159 THR cc_start: 0.6321 (OUTLIER) cc_final: 0.5922 (p) REVERT: K 48 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6933 (mmp-170) REVERT: K 168 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7377 (mttt) REVERT: K 203 LEU cc_start: 0.6506 (mp) cc_final: 0.5712 (mt) REVERT: L 28 LYS cc_start: 0.8335 (mttt) cc_final: 0.8066 (mttm) REVERT: M 143 TYR cc_start: 0.8817 (p90) cc_final: 0.8547 (p90) REVERT: M 149 ASP cc_start: 0.7788 (t0) cc_final: 0.7522 (t0) REVERT: N 13 MET cc_start: 0.7664 (tpp) cc_final: 0.6651 (mpp) REVERT: N 14 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6647 (ttp80) REVERT: N 24 ILE cc_start: 0.8238 (mm) cc_final: 0.8022 (mt) REVERT: P 330 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (p0) REVERT: Q 339 ASP cc_start: 0.8438 (m-30) cc_final: 0.8139 (t70) REVERT: R 339 ASP cc_start: 0.8749 (t0) cc_final: 0.8424 (t0) REVERT: S 361 VAL cc_start: 0.9034 (t) cc_final: 0.8774 (t) REVERT: S 509 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7280 (ttt180) REVERT: T 339 ASP cc_start: 0.8405 (m-30) cc_final: 0.8068 (m-30) REVERT: T 509 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.6690 (tpt-90) REVERT: U 395 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6655 (mpt) REVERT: U 401 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8260 (tt) REVERT: U 430 ASN cc_start: 0.8463 (t0) cc_final: 0.8212 (t0) REVERT: W 325 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7864 (tmm) REVERT: W 430 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (t0) REVERT: W 507 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7333 (mm-30) REVERT: W 509 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7079 (ttp-170) REVERT: X 512 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7906 (mp0) REVERT: Y 395 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6171 (mpt) REVERT: Z 398 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7906 (mt) REVERT: Z 432 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: a 339 ASP cc_start: 0.8220 (p0) cc_final: 0.7894 (t70) REVERT: b 325 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7462 (mpp) REVERT: b 354 GLU cc_start: 0.8200 (tt0) cc_final: 0.7494 (pt0) REVERT: c 507 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: O 15 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6551 (mt-10) REVERT: O 51 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7896 (mm-40) outliers start: 118 outliers final: 62 residues processed: 612 average time/residue: 0.4684 time to fit residues: 356.1786 Evaluate side-chains 615 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 527 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 509 ARG Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain c residue 507 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 437 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 467 optimal weight: 0.3980 chunk 440 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 584 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 564 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN G 73 ASN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 105 GLN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN P 390 ASN R 415 GLN U 381 ASN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.090237 restraints weight = 56643.360| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.64 r_work: 0.2878 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 47066 Z= 0.135 Angle : 0.497 9.112 63704 Z= 0.264 Chirality : 0.043 0.198 7251 Planarity : 0.004 0.052 8400 Dihedral : 3.896 51.281 6856 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.46 % Allowed : 19.22 % Favored : 78.32 % 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: 2.92 (0.10), residues: 2562 sheet: 0.94 (0.14), residues: 1526 loop : 0.03 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 14 TYR 0.019 0.001 TYR I 118 PHE 0.032 0.002 PHE M 71 TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 Details of bonding type rmsd covalent geometry : bond 0.00312 (47066) covalent geometry : angle 0.49671 (63704) hydrogen bonds : bond 0.03345 ( 3042) hydrogen bonds : angle 4.12302 ( 8718) *********************** 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 644 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 530 time to evaluate : 1.060 Fit side-chains REVERT: A 51 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8045 (mm-40) REVERT: A 161 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7303 (mp0) REVERT: C 13 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5291 (mmt) REVERT: C 132 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: D 21 ARG cc_start: 0.6587 (mtt90) cc_final: 0.6385 (mmt-90) REVERT: E 13 MET cc_start: 0.5899 (mmm) cc_final: 0.4791 (mmp) REVERT: E 22 LYS cc_start: 0.7453 (mtpt) cc_final: 0.6765 (ptpp) REVERT: E 80 GLN cc_start: 0.8526 (tp40) cc_final: 0.8176 (tp-100) REVERT: E 135 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6992 (ptm160) REVERT: E 165 ASN cc_start: 0.5664 (m-40) cc_final: 0.5423 (m110) REVERT: E 219 ARG cc_start: 0.8563 (tmm-80) cc_final: 0.8141 (ttp-110) REVERT: F 80 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: F 116 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5251 (tmmt) REVERT: F 168 LYS cc_start: 0.6352 (mmmm) cc_final: 0.5989 (mtmt) REVERT: G 119 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: G 169 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5447 (tp30) REVERT: G 176 SER cc_start: 0.7406 (m) cc_final: 0.6937 (p) REVERT: G 233 LEU cc_start: 0.7204 (mp) cc_final: 0.6890 (tp) REVERT: H 33 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7480 (pp) REVERT: H 152 HIS cc_start: 0.7408 (m90) cc_final: 0.7087 (m90) REVERT: H 174 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7593 (t0) REVERT: I 13 MET cc_start: 0.6446 (mmm) cc_final: 0.6120 (mmt) REVERT: I 22 LYS cc_start: 0.6573 (mtmt) cc_final: 0.5863 (mmpt) REVERT: I 70 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: I 159 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.5913 (p) REVERT: K 48 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6937 (mmp-170) REVERT: K 168 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7407 (mttt) REVERT: K 203 LEU cc_start: 0.6529 (mp) cc_final: 0.5750 (mt) REVERT: L 28 LYS cc_start: 0.8349 (mttt) cc_final: 0.8083 (mttm) REVERT: M 143 TYR cc_start: 0.8829 (p90) cc_final: 0.8563 (p90) REVERT: M 149 ASP cc_start: 0.7788 (t0) cc_final: 0.7516 (t0) REVERT: N 13 MET cc_start: 0.7684 (tpp) cc_final: 0.6664 (mpp) REVERT: N 14 ARG cc_start: 0.7080 (ttp-110) cc_final: 0.6617 (ttp80) REVERT: N 24 ILE cc_start: 0.8283 (mm) cc_final: 0.8082 (mt) REVERT: P 330 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (p0) REVERT: Q 339 ASP cc_start: 0.8433 (m-30) cc_final: 0.8159 (t70) REVERT: Q 519 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: R 339 ASP cc_start: 0.8706 (t0) cc_final: 0.8344 (t0) REVERT: S 361 VAL cc_start: 0.9008 (t) cc_final: 0.8759 (t) REVERT: S 509 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7262 (ttt180) REVERT: T 339 ASP cc_start: 0.8377 (m-30) cc_final: 0.8166 (m-30) REVERT: T 509 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6659 (tpt-90) REVERT: U 395 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6700 (mpt) REVERT: U 430 ASN cc_start: 0.8464 (t0) cc_final: 0.8208 (t0) REVERT: U 434 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: W 325 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: W 430 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8143 (t0) REVERT: W 507 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7327 (mm-30) REVERT: W 509 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7113 (ttp-170) REVERT: X 512 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7881 (mp0) REVERT: Y 395 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6204 (mpt) REVERT: Z 398 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7917 (mt) REVERT: Z 432 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: a 339 ASP cc_start: 0.8236 (p0) cc_final: 0.7898 (t70) REVERT: b 325 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7500 (mpp) REVERT: c 507 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: O 15 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6519 (mt-10) REVERT: O 51 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7898 (mm-40) outliers start: 114 outliers final: 64 residues processed: 602 average time/residue: 0.4672 time to fit residues: 349.5913 Evaluate side-chains 611 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 520 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 174 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 399 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain V residue 401 LEU Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain c residue 507 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 0.0670 chunk 509 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 543 optimal weight: 5.9990 chunk 364 optimal weight: 7.9990 chunk 446 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 485 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN G 73 ASN G 152 HIS H 45 ASN H 80 GLN I 101 ASN J 165 ASN K 216 ASN L 101 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 390 ASN R 415 GLN V 324 ASN Z 322 GLN c 322 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.088228 restraints weight = 56949.719| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.66 r_work: 0.2761 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 47066 Z= 0.206 Angle : 0.560 9.497 63704 Z= 0.296 Chirality : 0.045 0.332 7251 Planarity : 0.004 0.053 8400 Dihedral : 4.172 48.026 6856 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.31 % Allowed : 19.38 % Favored : 78.32 % 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: 2.06 (0.11), residues: 6048 helix: 2.72 (0.10), residues: 2548 sheet: 0.89 (0.14), residues: 1526 loop : -0.03 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 135 TYR 0.024 0.002 TYR N 118 PHE 0.036 0.003 PHE M 71 TRP 0.006 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 Details of bonding type rmsd covalent geometry : bond 0.00489 (47066) covalent geometry : angle 0.56018 (63704) hydrogen bonds : bond 0.03950 ( 3042) hydrogen bonds : angle 4.27576 ( 8718) ********************** 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 625 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 518 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: A 161 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7225 (mp0) REVERT: C 13 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5449 (mmt) REVERT: C 132 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: D 13 MET cc_start: 0.6224 (tpp) cc_final: 0.5336 (tmm) REVERT: D 21 ARG cc_start: 0.6567 (mtt90) cc_final: 0.6366 (mtt-85) REVERT: E 13 MET cc_start: 0.5960 (mmm) cc_final: 0.4792 (mmp) REVERT: E 14 ARG cc_start: 0.5648 (mtm110) cc_final: 0.5080 (ptp90) REVERT: E 80 GLN cc_start: 0.8553 (tp40) cc_final: 0.8198 (tp-100) REVERT: E 165 ASN cc_start: 0.5569 (m-40) cc_final: 0.5291 (m110) REVERT: E 219 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8133 (ttp-110) REVERT: F 80 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: F 116 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5273 (tmmt) REVERT: F 168 LYS cc_start: 0.6364 (mmmm) cc_final: 0.5987 (mtmt) REVERT: F 234 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6051 (pp) REVERT: G 119 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: G 176 SER cc_start: 0.7412 (m) cc_final: 0.6928 (p) REVERT: G 233 LEU cc_start: 0.7201 (mp) cc_final: 0.6903 (tp) REVERT: H 33 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7481 (pp) REVERT: H 174 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7736 (t0) REVERT: I 13 MET cc_start: 0.6442 (mmm) cc_final: 0.6096 (mmt) REVERT: I 70 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: I 159 THR cc_start: 0.6246 (OUTLIER) cc_final: 0.5859 (p) REVERT: K 48 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6805 (mmp-170) REVERT: K 168 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7382 (mttt) REVERT: K 203 LEU cc_start: 0.6580 (mp) cc_final: 0.5820 (mt) REVERT: L 28 LYS cc_start: 0.8331 (mttt) cc_final: 0.8065 (mttm) REVERT: M 143 TYR cc_start: 0.8854 (p90) cc_final: 0.8590 (p90) REVERT: M 149 ASP cc_start: 0.7838 (t0) cc_final: 0.7550 (t0) REVERT: N 13 MET cc_start: 0.7629 (tpp) cc_final: 0.6593 (mpp) REVERT: N 14 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6761 (ttp80) REVERT: N 113 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7736 (mp0) REVERT: P 330 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8182 (p0) REVERT: Q 339 ASP cc_start: 0.8541 (m-30) cc_final: 0.8256 (t70) REVERT: Q 519 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: R 339 ASP cc_start: 0.8718 (t0) cc_final: 0.8334 (t0) REVERT: S 361 VAL cc_start: 0.9083 (t) cc_final: 0.8817 (t) REVERT: T 461 ASP cc_start: 0.8065 (t0) cc_final: 0.7771 (t0) REVERT: T 509 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6733 (tpt-90) REVERT: U 395 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6719 (mpt) REVERT: U 430 ASN cc_start: 0.8447 (t0) cc_final: 0.8165 (t0) REVERT: U 434 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: W 325 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7911 (tmm) REVERT: W 507 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7419 (mm-30) REVERT: W 509 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7223 (ttp-170) REVERT: X 512 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7815 (mp0) REVERT: Y 395 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6228 (mpt) REVERT: Z 398 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7872 (mt) REVERT: Z 432 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: b 325 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7505 (mpp) REVERT: c 507 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: O 15 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6486 (mt-10) outliers start: 107 outliers final: 61 residues processed: 582 average time/residue: 0.4511 time to fit residues: 326.6786 Evaluate side-chains 587 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 501 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 174 ASN Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 322 GLN Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 341 THR Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 398 LEU Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain Z residue 512 GLU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain c residue 507 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 270 optimal weight: 0.2980 chunk 117 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 576 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 449 optimal weight: 0.9980 chunk 475 optimal weight: 1.9990 chunk 483 optimal weight: 0.7980 chunk 314 optimal weight: 0.7980 chunk 573 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN G 73 ASN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 322 GLN R 415 GLN V 324 ASN Z 322 GLN c 322 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.090666 restraints weight = 56655.897| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.65 r_work: 0.2872 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47066 Z= 0.116 Angle : 0.492 9.706 63704 Z= 0.262 Chirality : 0.042 0.230 7251 Planarity : 0.004 0.061 8400 Dihedral : 3.918 43.752 6856 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.13 % Allowed : 19.74 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.23 (0.11), residues: 6048 helix: 2.91 (0.10), residues: 2548 sheet: 0.91 (0.14), residues: 1526 loop : 0.03 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 135 TYR 0.017 0.001 TYR C 143 PHE 0.032 0.002 PHE M 71 TRP 0.004 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 Details of bonding type rmsd covalent geometry : bond 0.00262 (47066) covalent geometry : angle 0.49190 (63704) hydrogen bonds : bond 0.03243 ( 3042) hydrogen bonds : angle 4.16919 ( 8718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12070.31 seconds wall clock time: 205 minutes 59.00 seconds (12359.00 seconds total)