Starting phenix.real_space_refine on Thu Dec 26 16:05:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.map" model { file = "/net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6v_27223/12_2024/8d6v_27223.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29077 2.51 5 N 8225 2.21 5 O 8966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 26.56, per 1000 atoms: 0.57 Number of scatterers: 46380 At special positions: 0 Unit cell: (133.4, 136.88, 175.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 8966 8.00 N 8225 7.00 C 29077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.17 Conformation dependent library (CDL) restraints added in 6.2 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11158 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 70 sheets defined 46.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.810A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.552A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.629A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.522A pdb=" N LEU D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.557A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.660A pdb=" N ALA D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.660A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 removed outlier: 3.618A pdb=" N ALA E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.516A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.278A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 removed outlier: 3.538A pdb=" N ALA F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.552A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.183A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 removed outlier: 3.507A pdb=" N LEU I 99 " --> pdb=" O THR I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.383A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.694A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 removed outlier: 3.592A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.399A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 removed outlier: 3.617A pdb=" N ALA J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 234 Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.520A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.519A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 removed outlier: 3.594A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.430A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 removed outlier: 3.502A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.592A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.549A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 395 Processing helix chain 'P' and resid 413 through 416 removed outlier: 3.540A pdb=" N SER P 416 " --> pdb=" O ASP P 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 413 through 416' Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.871A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.666A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 removed outlier: 3.524A pdb=" N ASN Q 390 " --> pdb=" O MET Q 386 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 396 removed outlier: 3.517A pdb=" N GLN Q 396 " --> pdb=" O ALA Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.734A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.631A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 removed outlier: 3.511A pdb=" N ASN R 390 " --> pdb=" O MET R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 395 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.770A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.573A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 removed outlier: 3.523A pdb=" N ASN S 390 " --> pdb=" O MET S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 390 through 397 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.764A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.524A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 389 Processing helix chain 'T' and resid 390 through 396 removed outlier: 3.709A pdb=" N GLN T 396 " --> pdb=" O ALA T 392 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.825A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.678A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 389 Processing helix chain 'U' and resid 390 through 395 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.853A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.648A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 removed outlier: 3.518A pdb=" N ASN V 390 " --> pdb=" O MET V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 390 through 395 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.769A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.681A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 removed outlier: 3.586A pdb=" N ASN W 390 " --> pdb=" O MET W 386 " (cutoff:3.500A) Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 3.839A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.646A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.706A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.631A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.780A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 removed outlier: 3.635A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 397 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 3.791A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.625A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 removed outlier: 3.511A pdb=" N ASN a 390 " --> pdb=" O MET a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 390 through 395 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.797A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.597A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 removed outlier: 3.504A pdb=" N ASN b 390 " --> pdb=" O MET b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 390 through 395 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.784A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.634A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 395 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.782A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.621A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.610A pdb=" N LEU O 19 " --> pdb=" O GLU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.593A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.669A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.503A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.533A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.482A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.504A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.499A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.515A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.179A pdb=" N ILE H 53 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA H 64 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU H 55 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE H 62 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.488A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.458A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.487A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.559A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 153 through 156 removed outlier: 4.293A pdb=" N VAL M 210 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.498A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.535A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.511A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET P 325 " --> pdb=" O GLN P 322 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.780A pdb=" N VAL P 334 " --> pdb=" O ILE P 345 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE P 345 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE P 336 " --> pdb=" O THR P 343 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR P 343 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 436 through 440 Processing sheet with id=AD4, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.564A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET Q 325 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 335 removed outlier: 3.720A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AD7, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.651A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET R 325 " --> pdb=" O GLN R 322 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.703A pdb=" N VAL R 334 " --> pdb=" O ILE R 345 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE R 345 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE R 336 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR R 343 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE R 420 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE1, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.573A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.703A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 436 through 440 Processing sheet with id=AE4, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.525A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.597A pdb=" N VAL T 334 " --> pdb=" O ILE T 345 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE T 345 " --> pdb=" O VAL T 334 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE T 336 " --> pdb=" O THR T 343 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR T 343 " --> pdb=" O ILE T 336 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AE7, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.531A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET U 325 " --> pdb=" O GLN U 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.625A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.640A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.517A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.530A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.717A pdb=" N VAL W 334 " --> pdb=" O ILE W 345 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE W 345 " --> pdb=" O VAL W 334 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE W 336 " --> pdb=" O THR W 343 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR W 343 " --> pdb=" O ILE W 336 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.630A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 334 through 335 removed outlier: 3.870A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG1, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.593A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.652A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 436 through 440 Processing sheet with id=AG4, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.425A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE Z 326 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 334 through 335 removed outlier: 3.767A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG7, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.426A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.643A pdb=" N VAL a 334 " --> pdb=" O ILE a 345 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE a 345 " --> pdb=" O VAL a 334 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE a 336 " --> pdb=" O THR a 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR a 343 " --> pdb=" O ILE a 336 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.558A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.541A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 436 through 440 Processing sheet with id=AH4, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.548A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET c 325 " --> pdb=" O GLN c 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.697A pdb=" N VAL c 334 " --> pdb=" O ILE c 345 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE c 345 " --> pdb=" O VAL c 334 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE c 336 " --> pdb=" O THR c 343 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR c 343 " --> pdb=" O ILE c 336 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.471A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3023 hydrogen bonds defined for protein. 8631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.00 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12568 1.33 - 1.45: 7877 1.45 - 1.57: 26411 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N THR X 341 " pdb=" CA THR X 341 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.49e+00 bond pdb=" N THR R 341 " pdb=" CA THR R 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.30e+00 bond pdb=" N ILE Q 336 " pdb=" CA ILE Q 336 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.22e-02 6.72e+03 8.20e+00 bond pdb=" N THR Y 341 " pdb=" CA THR Y 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.17e+00 bond pdb=" N THR S 341 " pdb=" CA THR S 341 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.11e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 62515 1.82 - 3.65: 1100 3.65 - 5.47: 84 5.47 - 7.29: 4 7.29 - 9.12: 1 Bond angle restraints: 63704 Sorted by residual: angle pdb=" N ARG O 16 " pdb=" CA ARG O 16 " pdb=" C ARG O 16 " ideal model delta sigma weight residual 112.90 107.75 5.15 1.31e+00 5.83e-01 1.55e+01 angle pdb=" O TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 120.71 124.20 -3.49 9.00e-01 1.23e+00 1.50e+01 angle pdb=" CA PRO R 414 " pdb=" N PRO R 414 " pdb=" CD PRO R 414 " ideal model delta sigma weight residual 112.00 106.72 5.28 1.40e+00 5.10e-01 1.42e+01 angle pdb=" CA TYR E 89 " pdb=" C TYR E 89 " pdb=" N ASP E 90 " ideal model delta sigma weight residual 119.56 117.42 2.14 5.80e-01 2.97e+00 1.36e+01 angle pdb=" N GLY O 66 " pdb=" CA GLY O 66 " pdb=" C GLY O 66 " ideal model delta sigma weight residual 110.29 114.49 -4.20 1.28e+00 6.10e-01 1.08e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 26209 18.10 - 36.19: 1669 36.19 - 54.29: 349 54.29 - 72.39: 60 72.39 - 90.48: 48 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL G 212 " pdb=" C VAL G 212 " pdb=" N LEU G 213 " pdb=" CA LEU G 213 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL H 212 " pdb=" C VAL H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA VAL K 212 " pdb=" C VAL K 212 " pdb=" N LEU K 213 " pdb=" CA LEU K 213 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5570 0.048 - 0.095: 1281 0.095 - 0.143: 387 0.143 - 0.191: 6 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ILE Z 336 " pdb=" N ILE Z 336 " pdb=" C ILE Z 336 " pdb=" CB ILE Z 336 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE Q 336 " pdb=" N ILE Q 336 " pdb=" C ILE Q 336 " pdb=" CB ILE Q 336 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE b 336 " pdb=" N ILE b 336 " pdb=" C ILE b 336 " pdb=" CB ILE b 336 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 413 " 0.086 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO R 414 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO R 414 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO R 414 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 135 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO I 136 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I 136 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 136 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 135 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO H 136 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " -0.029 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3898 2.74 - 3.28: 43587 3.28 - 3.82: 76895 3.82 - 4.36: 89776 4.36 - 4.90: 163022 Nonbonded interactions: 377178 Sorted by model distance: nonbonded pdb=" OD1 ASP V 338 " pdb=" OG1 THR V 341 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP W 338 " pdb=" OG1 THR W 341 " model vdw 2.223 3.040 nonbonded pdb=" OG SER Z 422 " pdb=" OE2 GLU Z 432 " model vdw 2.234 3.040 nonbonded pdb=" O ILE E 147 " pdb=" NE2 GLN e 172 " model vdw 2.235 3.120 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.245 3.040 ... (remaining 377173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.060 Extract box with map and model: 1.940 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 110.500 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47066 Z= 0.231 Angle : 0.572 9.118 63704 Z= 0.341 Chirality : 0.044 0.239 7251 Planarity : 0.004 0.128 8400 Dihedral : 13.295 90.483 17177 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.11), residues: 6048 helix: 2.83 (0.10), residues: 2548 sheet: 0.83 (0.13), residues: 1484 loop : 0.06 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.005 0.001 HIS b 365 PHE 0.029 0.002 PHE J 71 TYR 0.021 0.001 TYR M 118 ARG 0.011 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 685 time to evaluate : 4.920 Fit side-chains REVERT: A 17 SER cc_start: 0.8551 (m) cc_final: 0.8296 (m) REVERT: A 80 GLN cc_start: 0.8468 (mt0) cc_final: 0.8020 (mt0) REVERT: C 14 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6700 (mtm-85) REVERT: D 174 ASN cc_start: 0.7227 (m-40) cc_final: 0.6593 (t0) REVERT: E 106 THR cc_start: 0.8420 (t) cc_final: 0.7967 (p) REVERT: G 29 SER cc_start: 0.7815 (m) cc_final: 0.7549 (m) REVERT: G 109 THR cc_start: 0.7922 (m) cc_final: 0.7722 (m) REVERT: J 80 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7670 (tp40) REVERT: J 156 MET cc_start: 0.8899 (mtm) cc_final: 0.8603 (mtm) REVERT: K 93 ASP cc_start: 0.8967 (m-30) cc_final: 0.8623 (m-30) REVERT: L 29 SER cc_start: 0.9334 (m) cc_final: 0.9126 (m) REVERT: L 47 SER cc_start: 0.8588 (m) cc_final: 0.8379 (m) REVERT: M 22 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7606 (mtmt) REVERT: R 503 VAL cc_start: 0.8826 (m) cc_final: 0.8527 (p) REVERT: V 354 GLU cc_start: 0.7587 (tt0) cc_final: 0.7265 (tt0) REVERT: X 444 LEU cc_start: 0.8677 (mp) cc_final: 0.8476 (mp) REVERT: Y 458 THR cc_start: 0.8330 (p) cc_final: 0.8053 (p) REVERT: O 93 ASP cc_start: 0.9004 (m-30) cc_final: 0.8785 (m-30) outliers start: 0 outliers final: 0 residues processed: 685 average time/residue: 0.6166 time to fit residues: 695.8745 Evaluate side-chains 585 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.0060 chunk 456 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 155 optimal weight: 0.0770 chunk 307 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 471 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 546 optimal weight: 0.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN F 216 ASN G 80 GLN K 105 GLN L 80 GLN M 45 ASN M 80 GLN N 45 ASN P 322 GLN R 322 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 47066 Z= 0.150 Angle : 0.466 7.388 63704 Z= 0.250 Chirality : 0.042 0.171 7251 Planarity : 0.003 0.048 8400 Dihedral : 3.598 24.617 6853 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.69 % Allowed : 5.43 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.11), residues: 6048 helix: 2.99 (0.10), residues: 2576 sheet: 0.94 (0.14), residues: 1484 loop : 0.07 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS V 365 PHE 0.038 0.002 PHE N 71 TYR 0.010 0.001 TYR b 359 ARG 0.007 0.000 ARG G 21 *********************** 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 640 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 608 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8577 (m) cc_final: 0.8340 (m) REVERT: E 105 GLN cc_start: 0.7396 (tp40) cc_final: 0.7105 (tp40) REVERT: G 29 SER cc_start: 0.7575 (m) cc_final: 0.7059 (p) REVERT: G 109 THR cc_start: 0.7994 (m) cc_final: 0.7707 (m) REVERT: H 143 TYR cc_start: 0.7460 (p90) cc_final: 0.7207 (p90) REVERT: I 133 THR cc_start: 0.8266 (t) cc_final: 0.8042 (m) REVERT: L 156 MET cc_start: 0.8744 (mtm) cc_final: 0.8364 (mtm) REVERT: N 14 ARG cc_start: 0.7475 (ttp-110) cc_final: 0.6959 (ttp-110) REVERT: N 24 ILE cc_start: 0.8610 (mm) cc_final: 0.8260 (mm) REVERT: N 83 ASP cc_start: 0.8739 (m-30) cc_final: 0.8527 (m-30) REVERT: P 333 LYS cc_start: 0.8907 (mttt) cc_final: 0.8652 (mtmt) REVERT: Q 314 MET cc_start: 0.8735 (ttt) cc_final: 0.8535 (ttt) REVERT: R 503 VAL cc_start: 0.8796 (m) cc_final: 0.8536 (p) REVERT: U 355 PHE cc_start: 0.8183 (m-10) cc_final: 0.7959 (m-80) REVERT: Y 314 MET cc_start: 0.8870 (ttt) cc_final: 0.8616 (ttt) REVERT: a 307 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8549 (mtmt) outliers start: 32 outliers final: 21 residues processed: 621 average time/residue: 0.6911 time to fit residues: 715.1247 Evaluate side-chains 582 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 561 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 454 optimal weight: 1.9990 chunk 372 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 547 optimal weight: 1.9990 chunk 591 optimal weight: 5.9990 chunk 487 optimal weight: 2.9990 chunk 543 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 439 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 ASN G 80 GLN I 51 GLN K 105 GLN N 45 ASN P 322 GLN S 390 ASN U 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 47066 Z= 0.172 Angle : 0.458 7.409 63704 Z= 0.245 Chirality : 0.042 0.170 7251 Planarity : 0.003 0.045 8400 Dihedral : 3.562 23.675 6853 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.01 % Allowed : 7.46 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.11), residues: 6048 helix: 3.03 (0.10), residues: 2576 sheet: 0.86 (0.13), residues: 1526 loop : 0.10 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 429 HIS 0.004 0.001 HIS b 365 PHE 0.034 0.002 PHE A 71 TYR 0.011 0.001 TYR M 87 ARG 0.007 0.000 ARG G 21 *********************** 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 623 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 576 time to evaluate : 5.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8596 (m) cc_final: 0.8364 (m) REVERT: A 114 GLN cc_start: 0.8082 (tp40) cc_final: 0.7808 (tp40) REVERT: E 105 GLN cc_start: 0.7449 (tp40) cc_final: 0.7092 (tp40) REVERT: G 29 SER cc_start: 0.7567 (m) cc_final: 0.6951 (p) REVERT: G 109 THR cc_start: 0.8030 (m) cc_final: 0.7748 (m) REVERT: H 143 TYR cc_start: 0.7495 (p90) cc_final: 0.7227 (p90) REVERT: L 156 MET cc_start: 0.8769 (mtm) cc_final: 0.8404 (mtm) REVERT: M 22 LYS cc_start: 0.7958 (mtmt) cc_final: 0.7588 (mtmt) REVERT: N 14 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7097 (ttp-110) REVERT: N 83 ASP cc_start: 0.8751 (m-30) cc_final: 0.8543 (m-30) REVERT: N 167 LEU cc_start: 0.7916 (mt) cc_final: 0.7711 (mt) REVERT: Q 314 MET cc_start: 0.8821 (ttt) cc_final: 0.8593 (ttt) REVERT: R 503 VAL cc_start: 0.8807 (m) cc_final: 0.8538 (p) REVERT: S 395 MET cc_start: 0.7016 (mmm) cc_final: 0.6469 (mmt) REVERT: U 355 PHE cc_start: 0.8275 (m-10) cc_final: 0.8069 (m-80) REVERT: Z 364 GLU cc_start: 0.7932 (tt0) cc_final: 0.7615 (tp30) outliers start: 47 outliers final: 38 residues processed: 596 average time/residue: 0.6172 time to fit residues: 607.1841 Evaluate side-chains 592 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 554 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain Q residue 338 ASP Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 4.9990 chunk 411 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 549 optimal weight: 0.9980 chunk 581 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 520 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 216 ASN G 80 GLN K 105 GLN M 45 ASN P 322 GLN U 324 ASN ** W 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 47066 Z= 0.266 Angle : 0.500 7.917 63704 Z= 0.266 Chirality : 0.044 0.188 7251 Planarity : 0.004 0.045 8400 Dihedral : 3.733 26.256 6853 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.36 % Allowed : 8.34 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.11), residues: 6048 helix: 2.91 (0.10), residues: 2576 sheet: 0.95 (0.14), residues: 1484 loop : -0.05 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 429 HIS 0.005 0.001 HIS S 365 PHE 0.035 0.003 PHE J 71 TYR 0.013 0.001 TYR J 87 ARG 0.011 0.000 ARG J 26 *********************** 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 636 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 573 time to evaluate : 5.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7175 (mmt) cc_final: 0.6764 (mmt) REVERT: A 17 SER cc_start: 0.8602 (m) cc_final: 0.8377 (m) REVERT: A 156 MET cc_start: 0.8822 (mtm) cc_final: 0.8207 (mtt) REVERT: C 24 ILE cc_start: 0.7690 (mt) cc_final: 0.7475 (mt) REVERT: E 105 GLN cc_start: 0.7518 (tp40) cc_final: 0.7149 (tp40) REVERT: E 140 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6681 (ttm-80) REVERT: G 109 THR cc_start: 0.8020 (m) cc_final: 0.7774 (m) REVERT: H 73 ASN cc_start: 0.7714 (t0) cc_final: 0.7324 (m-40) REVERT: H 143 TYR cc_start: 0.7440 (p90) cc_final: 0.7199 (p90) REVERT: H 156 MET cc_start: 0.7987 (mtm) cc_final: 0.7440 (mtm) REVERT: L 24 ILE cc_start: 0.8574 (mt) cc_final: 0.8363 (mp) REVERT: L 156 MET cc_start: 0.8823 (mtm) cc_final: 0.8440 (mtm) REVERT: M 22 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7550 (mtmt) REVERT: N 14 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.7002 (ttp-110) REVERT: N 24 ILE cc_start: 0.8695 (mm) cc_final: 0.8242 (mt) REVERT: V 461 ASP cc_start: 0.7042 (m-30) cc_final: 0.6841 (t0) REVERT: Z 364 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: a 324 ASN cc_start: 0.7876 (m-40) cc_final: 0.7645 (m-40) REVERT: c 430 ASN cc_start: 0.7809 (t0) cc_final: 0.7600 (t0) outliers start: 63 outliers final: 52 residues processed: 599 average time/residue: 0.6678 time to fit residues: 678.3196 Evaluate side-chains 605 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 551 time to evaluate : 7.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain U residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 433 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 496 optimal weight: 0.7980 chunk 402 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 297 optimal weight: 0.0470 chunk 522 optimal weight: 0.0270 chunk 146 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 GLN G 80 GLN K 105 GLN L 80 GLN M 45 ASN P 322 GLN S 390 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 47066 Z= 0.135 Angle : 0.434 9.096 63704 Z= 0.234 Chirality : 0.042 0.167 7251 Planarity : 0.003 0.042 8400 Dihedral : 3.512 22.498 6853 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.97 % Allowed : 9.59 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.11), residues: 6048 helix: 3.09 (0.10), residues: 2590 sheet: 0.90 (0.13), residues: 1526 loop : 0.04 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 429 HIS 0.003 0.001 HIS b 365 PHE 0.032 0.002 PHE I 71 TYR 0.008 0.001 TYR Z 359 ARG 0.006 0.000 ARG G 182 *********************** 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 615 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 570 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8631 (m) cc_final: 0.8391 (m) REVERT: C 24 ILE cc_start: 0.7654 (mt) cc_final: 0.7435 (mt) REVERT: E 105 GLN cc_start: 0.7451 (tp40) cc_final: 0.7059 (tp40) REVERT: E 140 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6604 (ttm-80) REVERT: G 109 THR cc_start: 0.8033 (m) cc_final: 0.7756 (m) REVERT: H 143 TYR cc_start: 0.7386 (p90) cc_final: 0.7139 (p90) REVERT: I 135 ARG cc_start: 0.7483 (ptm160) cc_final: 0.7164 (mmm-85) REVERT: L 24 ILE cc_start: 0.8500 (mt) cc_final: 0.8265 (mp) REVERT: M 22 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7666 (mtmt) REVERT: M 165 ASN cc_start: 0.7856 (m-40) cc_final: 0.7637 (m110) REVERT: N 14 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7025 (ttp-110) REVERT: N 167 LEU cc_start: 0.7887 (mt) cc_final: 0.7687 (mt) REVERT: R 307 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8396 (mtpt) REVERT: S 320 SER cc_start: 0.9043 (p) cc_final: 0.8807 (m) REVERT: S 395 MET cc_start: 0.6867 (mmm) cc_final: 0.6442 (mmt) REVERT: X 345 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8878 (mm) REVERT: Z 364 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: a 324 ASN cc_start: 0.7714 (m-40) cc_final: 0.7477 (m-40) REVERT: O 183 ILE cc_start: 0.7683 (mt) cc_final: 0.7475 (mt) outliers start: 45 outliers final: 39 residues processed: 587 average time/residue: 0.6026 time to fit residues: 583.7497 Evaluate side-chains 598 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 556 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.6980 chunk 524 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 341 optimal weight: 0.1980 chunk 143 optimal weight: 0.9990 chunk 582 optimal weight: 0.6980 chunk 483 optimal weight: 0.0270 chunk 269 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN G 80 GLN G 165 ASN K 105 GLN P 322 GLN S 390 ASN S 396 GLN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 47066 Z= 0.132 Angle : 0.428 8.136 63704 Z= 0.230 Chirality : 0.041 0.167 7251 Planarity : 0.003 0.041 8400 Dihedral : 3.426 20.858 6853 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.23 % Allowed : 10.00 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.11), residues: 6048 helix: 3.18 (0.10), residues: 2590 sheet: 1.07 (0.13), residues: 1596 loop : -0.11 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS b 365 PHE 0.031 0.002 PHE I 71 TYR 0.008 0.001 TYR D 139 ARG 0.006 0.000 ARG G 182 *********************** 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 637 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 580 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8651 (m) cc_final: 0.8415 (m) REVERT: D 174 ASN cc_start: 0.6790 (m110) cc_final: 0.6371 (t0) REVERT: E 140 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6545 (ttm170) REVERT: F 135 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7307 (ttp-170) REVERT: G 109 THR cc_start: 0.8006 (m) cc_final: 0.7734 (m) REVERT: H 143 TYR cc_start: 0.7365 (p90) cc_final: 0.7123 (p90) REVERT: I 135 ARG cc_start: 0.7493 (ptm160) cc_final: 0.7178 (mmm-85) REVERT: J 80 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7739 (tm-30) REVERT: J 233 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7754 (tp) REVERT: L 24 ILE cc_start: 0.8513 (mt) cc_final: 0.8240 (mp) REVERT: M 22 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7786 (mtmt) REVERT: N 14 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.7075 (ttp-110) REVERT: N 24 ILE cc_start: 0.8534 (mm) cc_final: 0.8200 (mt) REVERT: R 307 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8499 (mtpt) REVERT: X 345 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8876 (mm) REVERT: Z 364 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: a 324 ASN cc_start: 0.7712 (m-40) cc_final: 0.7483 (m-40) REVERT: O 183 ILE cc_start: 0.7796 (mt) cc_final: 0.7596 (mt) outliers start: 57 outliers final: 43 residues processed: 603 average time/residue: 0.6150 time to fit residues: 613.9354 Evaluate side-chains 605 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 558 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 338 ASP Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 425 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 490 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 chunk 580 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 353 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 GLN G 80 GLN K 105 GLN P 322 GLN Q 381 ASN T 324 ASN ** W 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 47066 Z= 0.254 Angle : 0.494 11.009 63704 Z= 0.262 Chirality : 0.043 0.185 7251 Planarity : 0.004 0.042 8400 Dihedral : 3.672 22.382 6853 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.34 % Allowed : 10.43 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.11), residues: 6048 helix: 2.97 (0.10), residues: 2590 sheet: 1.01 (0.14), residues: 1484 loop : -0.11 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 429 HIS 0.004 0.001 HIS b 365 PHE 0.034 0.003 PHE I 71 TYR 0.012 0.001 TYR J 87 ARG 0.007 0.000 ARG G 21 *********************** 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 647 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 585 time to evaluate : 4.161 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8649 (m) cc_final: 0.8408 (m) REVERT: D 174 ASN cc_start: 0.7054 (m110) cc_final: 0.6515 (t0) REVERT: E 140 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6489 (ttm170) REVERT: F 111 PHE cc_start: 0.7618 (t80) cc_final: 0.7117 (t80) REVERT: G 109 THR cc_start: 0.8053 (m) cc_final: 0.7793 (m) REVERT: H 73 ASN cc_start: 0.7718 (t0) cc_final: 0.7333 (m-40) REVERT: H 167 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5500 (mp) REVERT: I 135 ARG cc_start: 0.7487 (ptm160) cc_final: 0.7163 (mmm-85) REVERT: J 80 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7736 (tm-30) REVERT: J 233 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7726 (tp) REVERT: K 234 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6500 (tp) REVERT: L 24 ILE cc_start: 0.8560 (mt) cc_final: 0.8336 (mt) REVERT: M 22 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7695 (mtmt) REVERT: N 14 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7036 (ttp-110) REVERT: N 24 ILE cc_start: 0.8628 (mm) cc_final: 0.8375 (mt) REVERT: S 395 MET cc_start: 0.6856 (mmm) cc_final: 0.6446 (mmt) REVERT: W 367 GLU cc_start: 0.8123 (tt0) cc_final: 0.7806 (tt0) REVERT: X 345 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8913 (mm) REVERT: Y 434 GLU cc_start: 0.7467 (pt0) cc_final: 0.7194 (pt0) REVERT: a 324 ASN cc_start: 0.7857 (m-40) cc_final: 0.7604 (m-40) REVERT: c 430 ASN cc_start: 0.7812 (t0) cc_final: 0.7561 (t0) REVERT: O 114 GLN cc_start: 0.8267 (mt0) cc_final: 0.7878 (mt0) outliers start: 62 outliers final: 51 residues processed: 613 average time/residue: 0.6353 time to fit residues: 650.6126 Evaluate side-chains 618 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 562 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 458 THR Chi-restraints excluded: chain Z residue 401 LEU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Chi-restraints excluded: chain c residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 368 optimal weight: 0.8980 chunk 395 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 54 optimal weight: 0.0030 chunk 456 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN G 80 GLN K 105 GLN P 322 GLN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 47066 Z= 0.161 Angle : 0.452 10.092 63704 Z= 0.242 Chirality : 0.042 0.169 7251 Planarity : 0.003 0.041 8400 Dihedral : 3.552 21.554 6853 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.25 % Allowed : 11.01 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.11), residues: 6048 helix: 3.08 (0.10), residues: 2590 sheet: 0.92 (0.13), residues: 1526 loop : -0.01 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 429 HIS 0.003 0.001 HIS a 365 PHE 0.031 0.002 PHE I 71 TYR 0.011 0.001 TYR N 130 ARG 0.007 0.000 ARG G 21 *********************** 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 629 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 571 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8645 (m) cc_final: 0.8407 (m) REVERT: D 174 ASN cc_start: 0.7052 (m110) cc_final: 0.6493 (t0) REVERT: E 140 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6474 (ttm170) REVERT: E 156 MET cc_start: 0.8341 (mtm) cc_final: 0.8052 (mtm) REVERT: F 111 PHE cc_start: 0.7596 (t80) cc_final: 0.7074 (t80) REVERT: G 18 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5868 (mt-10) REVERT: G 109 THR cc_start: 0.7962 (m) cc_final: 0.7709 (m) REVERT: H 167 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5476 (mp) REVERT: I 135 ARG cc_start: 0.7482 (ptm160) cc_final: 0.7169 (mmm-85) REVERT: J 233 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7710 (tp) REVERT: K 234 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6708 (tp) REVERT: L 24 ILE cc_start: 0.8485 (mt) cc_final: 0.8243 (mt) REVERT: M 22 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7653 (mtmt) REVERT: M 165 ASN cc_start: 0.7908 (m-40) cc_final: 0.7696 (m110) REVERT: N 14 ARG cc_start: 0.7424 (ttp-110) cc_final: 0.7031 (ttp-110) REVERT: N 24 ILE cc_start: 0.8588 (mm) cc_final: 0.8324 (mt) REVERT: S 395 MET cc_start: 0.6796 (mmm) cc_final: 0.6378 (mmt) REVERT: W 367 GLU cc_start: 0.8107 (tt0) cc_final: 0.7798 (tt0) REVERT: X 345 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8880 (mm) REVERT: Z 364 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7464 (tp30) REVERT: a 324 ASN cc_start: 0.7786 (m-40) cc_final: 0.7543 (m-40) REVERT: a 390 ASN cc_start: 0.8763 (t0) cc_final: 0.8427 (t0) outliers start: 58 outliers final: 44 residues processed: 595 average time/residue: 0.5506 time to fit residues: 540.7424 Evaluate side-chains 602 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 552 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 395 MET Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 0.9980 chunk 555 optimal weight: 0.0870 chunk 507 optimal weight: 0.6980 chunk 540 optimal weight: 0.9990 chunk 325 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 424 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 488 optimal weight: 0.9980 chunk 511 optimal weight: 0.5980 chunk 538 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN G 80 GLN K 105 GLN P 322 GLN S 390 ASN T 324 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 47066 Z= 0.150 Angle : 0.451 10.041 63704 Z= 0.240 Chirality : 0.042 0.170 7251 Planarity : 0.003 0.041 8400 Dihedral : 3.493 21.132 6853 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.23 % Allowed : 10.95 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.11), residues: 6048 helix: 3.12 (0.10), residues: 2590 sheet: 1.05 (0.13), residues: 1596 loop : -0.17 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS a 365 PHE 0.031 0.002 PHE I 71 TYR 0.007 0.001 TYR Z 359 ARG 0.014 0.000 ARG L 14 *********************** 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 625 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 568 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8662 (m) cc_final: 0.8427 (m) REVERT: A 51 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8154 (mm-40) REVERT: D 174 ASN cc_start: 0.7029 (m110) cc_final: 0.6447 (t0) REVERT: E 140 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6455 (ttm170) REVERT: E 156 MET cc_start: 0.8323 (mtm) cc_final: 0.8021 (mtm) REVERT: F 111 PHE cc_start: 0.7598 (t80) cc_final: 0.7071 (t80) REVERT: G 18 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5877 (mt-10) REVERT: G 109 THR cc_start: 0.8036 (m) cc_final: 0.7762 (m) REVERT: H 167 LEU cc_start: 0.5776 (OUTLIER) cc_final: 0.5447 (mp) REVERT: I 135 ARG cc_start: 0.7476 (ptm160) cc_final: 0.7172 (mmm-85) REVERT: J 80 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7705 (tm-30) REVERT: J 233 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7709 (tp) REVERT: L 24 ILE cc_start: 0.8482 (mt) cc_final: 0.8240 (mt) REVERT: M 22 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7610 (mtmt) REVERT: N 14 ARG cc_start: 0.7397 (ttp-110) cc_final: 0.7010 (ttp-110) REVERT: N 24 ILE cc_start: 0.8579 (mm) cc_final: 0.8299 (mt) REVERT: S 395 MET cc_start: 0.6795 (mmm) cc_final: 0.6209 (mmt) REVERT: X 345 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (mm) REVERT: Y 432 GLU cc_start: 0.6617 (tp30) cc_final: 0.6191 (tp30) REVERT: Z 364 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: a 324 ASN cc_start: 0.7703 (m-40) cc_final: 0.7474 (m-40) REVERT: a 390 ASN cc_start: 0.8751 (t0) cc_final: 0.8434 (t0) outliers start: 57 outliers final: 46 residues processed: 592 average time/residue: 0.5451 time to fit residues: 535.0342 Evaluate side-chains 606 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 555 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 374 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Chi-restraints excluded: chain O residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 1.9990 chunk 571 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 397 optimal weight: 1.9990 chunk 599 optimal weight: 10.0000 chunk 551 optimal weight: 0.8980 chunk 477 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 368 optimal weight: 0.3980 chunk 292 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN E 105 GLN G 80 GLN K 105 GLN M 165 ASN P 322 GLN T 324 ASN ** Y 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1462 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= 0.162 Angle : 0.455 9.215 63704 Z= 0.243 Chirality : 0.042 0.171 7251 Planarity : 0.003 0.041 8400 Dihedral : 3.497 21.414 6853 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.16 % Allowed : 11.10 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.11), residues: 6048 helix: 3.10 (0.10), residues: 2590 sheet: 1.04 (0.13), residues: 1596 loop : -0.17 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS b 365 PHE 0.031 0.002 PHE I 71 TYR 0.008 0.001 TYR Y 335 ARG 0.008 0.000 ARG N 189 ********************** 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 611 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 557 time to evaluate : 4.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8674 (m) cc_final: 0.8446 (m) REVERT: A 51 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8173 (mm-40) REVERT: D 174 ASN cc_start: 0.7030 (m110) cc_final: 0.6424 (t0) REVERT: E 140 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6446 (ttm170) REVERT: E 156 MET cc_start: 0.8343 (mtm) cc_final: 0.7981 (mtm) REVERT: F 111 PHE cc_start: 0.7594 (t80) cc_final: 0.7064 (t80) REVERT: G 109 THR cc_start: 0.7994 (m) cc_final: 0.7738 (m) REVERT: H 167 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5494 (mp) REVERT: I 135 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7169 (mmm-85) REVERT: J 80 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7724 (tm-30) REVERT: J 233 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7699 (tp) REVERT: L 24 ILE cc_start: 0.8490 (mt) cc_final: 0.8241 (mt) REVERT: M 22 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7674 (mtmt) REVERT: N 24 ILE cc_start: 0.8583 (mm) cc_final: 0.8301 (mt) REVERT: S 395 MET cc_start: 0.6836 (mmm) cc_final: 0.6224 (mmt) REVERT: X 345 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8887 (mm) REVERT: Z 364 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: a 324 ASN cc_start: 0.7725 (m-40) cc_final: 0.7500 (m-40) REVERT: a 390 ASN cc_start: 0.8753 (t0) cc_final: 0.8429 (t0) REVERT: c 430 ASN cc_start: 0.7821 (t0) cc_final: 0.7594 (t0) outliers start: 54 outliers final: 49 residues processed: 580 average time/residue: 0.5530 time to fit residues: 530.6973 Evaluate side-chains 601 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 178 THR Chi-restraints excluded: chain P residue 325 MET Chi-restraints excluded: chain P residue 341 THR Chi-restraints excluded: chain R residue 401 LEU Chi-restraints excluded: chain S residue 364 GLU Chi-restraints excluded: chain S residue 399 LEU Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 341 THR Chi-restraints excluded: chain T residue 395 MET Chi-restraints excluded: chain T residue 401 LEU Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 322 GLN Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 341 THR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain X residue 503 VAL Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain b residue 401 LEU Chi-restraints excluded: chain b residue 447 LYS Chi-restraints excluded: chain b residue 458 THR Chi-restraints excluded: chain O residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 0.0570 chunk 508 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 440 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 478 optimal weight: 0.0030 chunk 200 optimal weight: 2.9990 chunk 491 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN E 105 GLN G 51 GLN G 80 GLN G 174 ASN H 11 GLN K 105 GLN P 322 GLN T 324 ASN ** Y 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.094131 restraints weight = 53131.556| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.64 r_work: 0.2789 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.105 47066 Z= 0.147 Angle : 0.546 59.196 63704 Z= 0.309 Chirality : 0.042 0.444 7251 Planarity : 0.003 0.040 8400 Dihedral : 3.502 23.423 6853 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.23 % Allowed : 11.08 % Favored : 87.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.11), residues: 6048 helix: 3.11 (0.10), residues: 2590 sheet: 1.04 (0.13), residues: 1596 loop : -0.16 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.003 0.001 HIS S 365 PHE 0.031 0.002 PHE I 71 TYR 0.007 0.001 TYR O 87 ARG 0.008 0.000 ARG L 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10599.46 seconds wall clock time: 190 minutes 21.55 seconds (11421.55 seconds total)