Starting phenix.real_space_refine on Thu Dec 26 16:19:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.map" model { file = "/net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6w_27224/12_2024/8d6w_27224.cif" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29077 2.51 5 N 8225 2.21 5 O 8966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.15s 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: 24.49, per 1000 atoms: 0.53 Number of scatterers: 46380 At special positions: 0 Unit cell: (134.964, 133.308, 170.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 8966 8.00 N 8225 7.00 C 29077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 6.0 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11158 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 70 sheets defined 46.5% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.39 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.517A pdb=" N VAL A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 114 removed outlier: 3.557A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.438A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.688A pdb=" N ALA A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.595A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.572A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 4.511A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.331A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 removed outlier: 3.535A pdb=" N ALA D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.392A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.507A pdb=" N VAL F 94 " --> pdb=" O ARG F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 114 removed outlier: 3.546A pdb=" N LEU F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.297A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 227 through 234 removed outlier: 3.699A pdb=" N GLN F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.519A pdb=" N LEU G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.493A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 removed outlier: 3.533A pdb=" N ALA G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 234 removed outlier: 3.585A pdb=" N GLN G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 removed outlier: 3.545A pdb=" N LEU H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.783A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 removed outlier: 3.942A pdb=" N ALA H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.539A pdb=" N PHE I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.690A pdb=" N VAL I 94 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.839A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 removed outlier: 3.859A pdb=" N ALA I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 removed outlier: 3.539A pdb=" N LEU J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.270A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 227 through 234 Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 removed outlier: 3.678A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.492A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.528A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 removed outlier: 3.506A pdb=" N LEU L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 removed outlier: 3.579A pdb=" N LEU M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.473A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.391A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 395 removed outlier: 4.799A pdb=" N ALA P 392 " --> pdb=" O ARG P 388 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 3.776A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.545A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 389 Processing helix chain 'Q' and resid 390 through 395 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 3.588A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.583A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 395 removed outlier: 4.686A pdb=" N ALA R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET R 395 " --> pdb=" O LEU R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 3.620A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.635A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 389 Processing helix chain 'S' and resid 390 through 397 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 3.724A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.588A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 389 Processing helix chain 'T' and resid 390 through 397 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 3.654A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.576A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 389 Processing helix chain 'U' and resid 390 through 396 removed outlier: 3.895A pdb=" N GLN U 396 " --> pdb=" O ALA U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 3.928A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.594A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 397 Processing helix chain 'V' and resid 442 through 454 removed outlier: 3.655A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.656A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 395 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 3.523A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.655A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 395 removed outlier: 4.666A pdb=" N ALA X 392 " --> pdb=" O ARG X 388 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA X 393 " --> pdb=" O GLY X 389 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 3.815A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.655A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 397 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 3.902A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 521 removed outlier: 3.558A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 389 Processing helix chain 'Z' and resid 390 through 397 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 3.685A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.657A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 389 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 3.671A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.545A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 389 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 442 through 454 removed outlier: 3.720A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.578A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 3.693A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.625A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.508A pdb=" N ARG O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 90 through 94 removed outlier: 3.590A pdb=" N VAL O 94 " --> pdb=" O ARG O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 114 removed outlier: 3.547A pdb=" N LEU O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.549A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 227 through 234 Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.487A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.452A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 removed outlier: 4.465A pdb=" N VAL D 210 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.464A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.511A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 removed outlier: 4.643A pdb=" N VAL F 210 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.507A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.453A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.475A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.406A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.519A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 153 through 156 removed outlier: 4.314A pdb=" N VAL K 210 " --> pdb=" O ILE K 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.496A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 153 through 156 removed outlier: 4.371A pdb=" N VAL L 210 " --> pdb=" O ILE L 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.509A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 153 through 156 removed outlier: 4.117A pdb=" N VAL M 210 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.421A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 153 through 156 removed outlier: 4.357A pdb=" N VAL N 210 " --> pdb=" O ILE N 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.510A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 436 through 440 Processing sheet with id=AD1, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.415A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.585A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 436 through 440 Processing sheet with id=AD4, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.431A pdb=" N GLN Q 322 " --> pdb=" O ILE Q 326 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE Q 326 " --> pdb=" O GLN Q 322 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.561A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE Q 420 " --> pdb=" O GLU Q 432 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 436 through 440 Processing sheet with id=AD7, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.477A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.633A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 436 through 440 Processing sheet with id=AE1, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.306A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET S 325 " --> pdb=" O GLN S 322 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.539A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE S 420 " --> pdb=" O GLU S 432 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 436 through 440 Processing sheet with id=AE4, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.400A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.551A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 436 through 440 Processing sheet with id=AE7, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.448A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.596A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 436 through 440 Processing sheet with id=AF1, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.375A pdb=" N GLN V 322 " --> pdb=" O ILE V 326 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.587A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 436 through 440 Processing sheet with id=AF4, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.377A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET W 325 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.470A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 436 through 440 Processing sheet with id=AF7, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.496A pdb=" N GLN X 322 " --> pdb=" O ILE X 326 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 334 through 338 removed outlier: 6.504A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 436 through 440 Processing sheet with id=AG1, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.485A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.562A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 436 through 440 Processing sheet with id=AG4, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.463A pdb=" N GLN Z 322 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE Z 326 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 334 through 336 removed outlier: 3.790A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 436 through 440 Processing sheet with id=AG7, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.302A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET a 325 " --> pdb=" O GLN a 322 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.463A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 436 through 440 Processing sheet with id=AH1, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.397A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.532A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 436 through 440 Processing sheet with id=AH4, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.456A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.583A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 153 through 156 removed outlier: 4.233A pdb=" N VAL O 210 " --> pdb=" O ILE O 225 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.484A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) 3042 hydrogen bonds defined for protein. 8718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.70 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15718 1.34 - 1.46: 7775 1.46 - 1.58: 23362 1.58 - 1.70: 1 1.70 - 1.82: 210 Bond restraints: 47066 Sorted by residual: bond pdb=" N VAL Y 439 " pdb=" CA VAL Y 439 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.15e-02 7.56e+03 1.18e+01 bond pdb=" N VAL D 30 " pdb=" CA VAL D 30 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N ILE R 420 " pdb=" CA ILE R 420 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.80e+00 bond pdb=" N VAL H 155 " pdb=" CA VAL H 155 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.20e-02 6.94e+03 9.76e+00 bond pdb=" N ILE c 431 " pdb=" CA ILE c 431 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.58e+00 ... (remaining 47061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 62437 1.85 - 3.70: 1126 3.70 - 5.55: 117 5.55 - 7.40: 19 7.40 - 9.24: 5 Bond angle restraints: 63704 Sorted by residual: angle pdb=" O TYR D 89 " pdb=" C TYR D 89 " pdb=" N ASP D 90 " ideal model delta sigma weight residual 120.83 124.17 -3.34 7.40e-01 1.83e+00 2.03e+01 angle pdb=" CA PRO D 151 " pdb=" N PRO D 151 " pdb=" CD PRO D 151 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" CA GLY H 157 " pdb=" C GLY H 157 " pdb=" O GLY H 157 " ideal model delta sigma weight residual 122.39 118.48 3.91 9.30e-01 1.16e+00 1.76e+01 angle pdb=" CA GLY b 418 " pdb=" C GLY b 418 " pdb=" O GLY b 418 " ideal model delta sigma weight residual 121.41 117.99 3.42 8.80e-01 1.29e+00 1.51e+01 angle pdb=" C GLN E 11 " pdb=" N ALA E 12 " pdb=" CA ALA E 12 " ideal model delta sigma weight residual 120.28 125.82 -5.54 1.44e+00 4.82e-01 1.48e+01 ... (remaining 63699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25314 17.99 - 35.97: 2275 35.97 - 53.96: 595 53.96 - 71.95: 104 71.95 - 89.93: 47 Dihedral angle restraints: 28335 sinusoidal: 10807 harmonic: 17528 Sorted by residual: dihedral pdb=" CA VAL A 212 " pdb=" C VAL A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL O 212 " pdb=" C VAL O 212 " pdb=" N LEU O 213 " pdb=" CA LEU O 213 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA VAL J 212 " pdb=" C VAL J 212 " pdb=" N LEU J 213 " pdb=" CA LEU J 213 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 28332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5513 0.048 - 0.096: 1299 0.096 - 0.144: 394 0.144 - 0.191: 38 0.191 - 0.239: 7 Chirality restraints: 7251 Sorted by residual: chirality pdb=" CA ALA E 12 " pdb=" N ALA E 12 " pdb=" C ALA E 12 " pdb=" CB ALA E 12 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL D 30 " pdb=" N VAL D 30 " pdb=" C VAL D 30 " pdb=" CB VAL D 30 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE c 420 " pdb=" N ILE c 420 " pdb=" C ILE c 420 " pdb=" CB ILE c 420 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 7248 not shown) Planarity restraints: 8400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Y 413 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO Y 414 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO Y 414 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO Y 414 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 118 " 0.028 2.00e-02 2.50e+03 2.10e-02 8.82e+00 pdb=" CG TYR I 118 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR I 118 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR I 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 118 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR I 118 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR I 118 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 118 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 150 " -0.041 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 151 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 8397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3238 2.74 - 3.28: 44324 3.28 - 3.82: 79864 3.82 - 4.36: 94799 4.36 - 4.90: 166365 Nonbonded interactions: 388590 Sorted by model distance: nonbonded pdb=" O ALA A 34 " pdb=" OH TYR A 171 " model vdw 2.197 3.040 nonbonded pdb=" OG SER E 29 " pdb=" O GLY E 157 " model vdw 2.198 3.040 nonbonded pdb=" O ALA G 166 " pdb=" OG SER G 170 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 142 " pdb=" OD1 ASP A 144 " model vdw 2.207 3.040 nonbonded pdb=" NH2 ARG R 329 " pdb=" O ASP a 476 " model vdw 2.209 3.120 ... (remaining 388585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.800 Check model and map are aligned: 0.320 Set scattering table: 0.410 Process input model: 108.010 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.560 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:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 47066 Z= 0.248 Angle : 0.599 9.244 63704 Z= 0.349 Chirality : 0.045 0.239 7251 Planarity : 0.004 0.096 8400 Dihedral : 15.251 89.932 17177 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.53 % Allowed : 13.28 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.11), residues: 6048 helix: 2.27 (0.10), residues: 2520 sheet: 0.79 (0.13), residues: 1526 loop : -0.21 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 429 HIS 0.004 0.001 HIS X 365 PHE 0.032 0.002 PHE M 71 TYR 0.049 0.001 TYR I 118 ARG 0.008 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 659 time to evaluate : 5.412 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8122 (mt0) cc_final: 0.7908 (mt0) REVERT: A 90 ASP cc_start: 0.8403 (t70) cc_final: 0.8159 (t70) REVERT: C 80 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7367 (mt0) REVERT: C 118 TYR cc_start: 0.7446 (m-10) cc_final: 0.7167 (m-10) REVERT: C 135 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6532 (mtt90) REVERT: D 134 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6768 (pptt) REVERT: E 80 GLN cc_start: 0.7959 (tp40) cc_final: 0.7745 (mm-40) REVERT: E 137 GLU cc_start: 0.6971 (mp0) cc_final: 0.6747 (pm20) REVERT: F 21 ARG cc_start: 0.6183 (ptp90) cc_final: 0.5843 (ttp-170) REVERT: F 53 ILE cc_start: 0.8437 (mm) cc_final: 0.8173 (mt) REVERT: F 209 GLU cc_start: 0.6787 (tt0) cc_final: 0.6559 (tt0) REVERT: G 26 ARG cc_start: 0.6949 (ptt-90) cc_final: 0.6669 (ptt180) REVERT: G 169 GLU cc_start: 0.6172 (mm-30) cc_final: 0.4988 (tp30) REVERT: H 67 LYS cc_start: 0.7607 (tttt) cc_final: 0.7362 (tttm) REVERT: H 121 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: H 152 HIS cc_start: 0.7231 (m90) cc_final: 0.6462 (m90) REVERT: I 70 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: I 153 PHE cc_start: 0.6840 (p90) cc_final: 0.6383 (p90) REVERT: I 159 THR cc_start: 0.6372 (p) cc_final: 0.5644 (t) REVERT: J 182 ARG cc_start: 0.6043 (mtt90) cc_final: 0.5784 (tpp-160) REVERT: J 214 ASP cc_start: 0.7895 (t0) cc_final: 0.7450 (t70) REVERT: M 13 MET cc_start: 0.7915 (mmm) cc_final: 0.7450 (mmp) REVERT: N 54 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8846 (p) REVERT: N 168 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7153 (tppt) REVERT: R 354 GLU cc_start: 0.7527 (tt0) cc_final: 0.7246 (tt0) REVERT: T 339 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: U 386 MET cc_start: 0.8922 (ttm) cc_final: 0.8692 (ttm) REVERT: V 364 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7587 (mt-10) REVERT: X 325 MET cc_start: 0.8055 (ttp) cc_final: 0.7575 (tpp) REVERT: Y 341 THR cc_start: 0.8949 (p) cc_final: 0.8674 (t) REVERT: Y 500 ASP cc_start: 0.8123 (m-30) cc_final: 0.7843 (m-30) REVERT: Z 324 ASN cc_start: 0.7863 (m-40) cc_final: 0.7504 (p0) REVERT: Z 500 ASP cc_start: 0.8269 (m-30) cc_final: 0.8044 (m-30) REVERT: c 325 MET cc_start: 0.8126 (ttp) cc_final: 0.7897 (tmt) outliers start: 71 outliers final: 23 residues processed: 708 average time/residue: 1.6487 time to fit residues: 1443.9937 Evaluate side-chains 558 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 531 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain T residue 339 ASP Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 409 ILE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain a residue 416 SER Chi-restraints excluded: chain a residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 4.9990 chunk 456 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 307 optimal weight: 0.7980 chunk 243 optimal weight: 0.0870 chunk 471 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 286 optimal weight: 0.7980 chunk 351 optimal weight: 3.9990 chunk 546 optimal weight: 4.9990 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 105 GLN C 73 ASN D 11 GLN D 51 GLN E 105 GLN E 165 ASN F 45 ASN F 51 GLN G 73 ASN H 80 GLN J 11 GLN J 73 ASN J 165 ASN K 216 ASN L 105 GLN L 165 ASN M 105 GLN N 45 ASN N 80 GLN P 322 GLN Q 390 ASN S 324 ASN S 390 ASN T 437 GLN U 365 HIS U 437 GLN V 437 GLN X 322 GLN X 456 GLN Y 437 GLN b 390 ASN c 322 GLN c 396 GLN d 172 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 47066 Z= 0.189 Angle : 0.501 8.050 63704 Z= 0.270 Chirality : 0.043 0.180 7251 Planarity : 0.004 0.061 8400 Dihedral : 4.572 100.660 6894 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.69 % Allowed : 14.85 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.11), residues: 6048 helix: 2.59 (0.10), residues: 2548 sheet: 0.87 (0.14), residues: 1526 loop : -0.07 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 429 HIS 0.005 0.001 HIS Q 365 PHE 0.037 0.002 PHE C 71 TYR 0.013 0.001 TYR J 171 ARG 0.018 0.000 ARG E 14 *********************** 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 716 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 591 time to evaluate : 5.891 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8331 (mmt90) REVERT: A 161 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7015 (mp0) REVERT: C 80 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7519 (mt0) REVERT: D 13 MET cc_start: 0.4689 (tmm) cc_final: 0.4476 (tpp) REVERT: D 113 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5956 (mp0) REVERT: E 13 MET cc_start: 0.6350 (mmm) cc_final: 0.5145 (mmp) REVERT: E 21 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6150 (tmm160) REVERT: E 80 GLN cc_start: 0.8079 (tp40) cc_final: 0.7745 (tp-100) REVERT: E 121 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: E 135 ARG cc_start: 0.7000 (ptm160) cc_final: 0.6662 (ptm160) REVERT: E 137 GLU cc_start: 0.7096 (mp0) cc_final: 0.6808 (mp0) REVERT: E 165 ASN cc_start: 0.5810 (m-40) cc_final: 0.5472 (m-40) REVERT: F 70 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: F 80 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: F 116 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5406 (tmmt) REVERT: G 73 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7204 (m110) REVERT: G 97 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6866 (ttm170) REVERT: G 176 SER cc_start: 0.7457 (m) cc_final: 0.7008 (p) REVERT: H 33 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7368 (pp) REVERT: H 152 HIS cc_start: 0.7230 (m90) cc_final: 0.6263 (m-70) REVERT: I 70 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: I 80 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8170 (tp40) REVERT: J 182 ARG cc_start: 0.5983 (mtt90) cc_final: 0.5746 (tpp-160) REVERT: K 168 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7362 (mttt) REVERT: K 203 LEU cc_start: 0.6666 (mp) cc_final: 0.5776 (mt) REVERT: M 26 ARG cc_start: 0.7793 (ptt-90) cc_final: 0.7504 (ptt90) REVERT: M 143 TYR cc_start: 0.8738 (p90) cc_final: 0.8451 (p90) REVERT: M 149 ASP cc_start: 0.7797 (t0) cc_final: 0.7537 (t0) REVERT: N 14 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.6359 (ttp80) REVERT: N 168 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7178 (tppt) REVERT: P 339 ASP cc_start: 0.7844 (t0) cc_final: 0.7491 (t0) REVERT: S 361 VAL cc_start: 0.8883 (t) cc_final: 0.8641 (t) REVERT: S 401 LEU cc_start: 0.8267 (mp) cc_final: 0.7970 (tp) REVERT: T 339 ASP cc_start: 0.8098 (m-30) cc_final: 0.7810 (m-30) REVERT: U 386 MET cc_start: 0.9059 (ttm) cc_final: 0.8850 (ttm) REVERT: U 395 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6318 (mpt) REVERT: X 325 MET cc_start: 0.8108 (ttp) cc_final: 0.7687 (tpp) REVERT: X 512 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: Y 341 THR cc_start: 0.9111 (p) cc_final: 0.8863 (t) REVERT: Z 324 ASN cc_start: 0.7859 (m-40) cc_final: 0.7442 (p0) REVERT: Z 500 ASP cc_start: 0.8428 (m-30) cc_final: 0.8194 (m-30) REVERT: c 325 MET cc_start: 0.8296 (ttp) cc_final: 0.7936 (ttp) REVERT: c 430 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.8015 (t0) REVERT: O 15 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: O 51 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7767 (mm-40) outliers start: 125 outliers final: 31 residues processed: 663 average time/residue: 1.6592 time to fit residues: 1361.0488 Evaluate side-chains 569 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 523 time to evaluate : 5.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 430 ASN Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 339 ASP Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 430 ASN Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 454 optimal weight: 3.9990 chunk 372 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 547 optimal weight: 9.9990 chunk 591 optimal weight: 7.9990 chunk 487 optimal weight: 5.9990 chunk 543 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 165 ASN C 73 ASN D 51 GLN F 45 ASN F 101 ASN H 80 GLN J 73 ASN J 165 ASN K 216 ASN L 165 ASN M 105 GLN N 45 ASN N 80 GLN P 322 GLN P 390 ASN S 324 ASN U 381 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN c 322 GLN O 80 GLN O 152 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 47066 Z= 0.258 Angle : 0.525 11.894 63704 Z= 0.278 Chirality : 0.044 0.185 7251 Planarity : 0.004 0.054 8400 Dihedral : 4.378 103.501 6862 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.06 % Allowed : 16.08 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.11), residues: 6048 helix: 2.65 (0.10), residues: 2548 sheet: 0.86 (0.13), residues: 1526 loop : -0.09 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP c 429 HIS 0.005 0.001 HIS X 365 PHE 0.034 0.003 PHE M 71 TYR 0.011 0.001 TYR J 171 ARG 0.011 0.000 ARG E 14 *********************** 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 694 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 552 time to evaluate : 5.206 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: A 161 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6996 (mp0) REVERT: C 132 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6284 (mt-10) REVERT: D 13 MET cc_start: 0.4880 (tmm) cc_final: 0.4634 (tpp) REVERT: D 113 GLU cc_start: 0.6335 (mt-10) cc_final: 0.6021 (mp0) REVERT: D 135 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6238 (ttp80) REVERT: E 13 MET cc_start: 0.6329 (mmm) cc_final: 0.5181 (mmp) REVERT: E 80 GLN cc_start: 0.8163 (tp40) cc_final: 0.7800 (tp-100) REVERT: E 112 THR cc_start: 0.7172 (m) cc_final: 0.6863 (t) REVERT: E 113 GLU cc_start: 0.5700 (tt0) cc_final: 0.5115 (mt-10) REVERT: E 114 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5427 (mm110) REVERT: E 165 ASN cc_start: 0.5716 (m-40) cc_final: 0.5430 (m-40) REVERT: F 29 SER cc_start: 0.6818 (m) cc_final: 0.6463 (p) REVERT: F 70 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: G 176 SER cc_start: 0.7651 (m) cc_final: 0.7093 (p) REVERT: H 33 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7360 (pp) REVERT: H 152 HIS cc_start: 0.7451 (m90) cc_final: 0.6595 (m90) REVERT: I 13 MET cc_start: 0.6677 (mmm) cc_final: 0.6376 (mmt) REVERT: I 153 PHE cc_start: 0.6899 (p90) cc_final: 0.6388 (p90) REVERT: I 159 THR cc_start: 0.6277 (p) cc_final: 0.5609 (t) REVERT: J 182 ARG cc_start: 0.5989 (mtt90) cc_final: 0.5767 (tpp-160) REVERT: K 203 LEU cc_start: 0.6604 (mp) cc_final: 0.5725 (mt) REVERT: M 80 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: M 143 TYR cc_start: 0.8816 (p90) cc_final: 0.8497 (p90) REVERT: M 149 ASP cc_start: 0.7744 (t0) cc_final: 0.7478 (t0) REVERT: N 14 ARG cc_start: 0.6781 (ttp-110) cc_final: 0.6477 (ttp80) REVERT: N 168 LYS cc_start: 0.8046 (ttmt) cc_final: 0.6996 (tptp) REVERT: P 330 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8129 (p0) REVERT: P 521 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7902 (mpt-90) REVERT: Q 354 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: S 361 VAL cc_start: 0.9067 (t) cc_final: 0.8790 (t) REVERT: T 339 ASP cc_start: 0.8109 (m-30) cc_final: 0.7846 (m-30) REVERT: U 395 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6412 (mpt) REVERT: U 401 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8216 (tt) REVERT: U 430 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8048 (t0) REVERT: W 325 MET cc_start: 0.8211 (tmt) cc_final: 0.7920 (tmm) REVERT: X 512 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: Y 398 LEU cc_start: 0.8284 (mt) cc_final: 0.8081 (mt) REVERT: a 325 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7747 (tmm) REVERT: a 340 TYR cc_start: 0.8946 (m-80) cc_final: 0.8666 (m-80) REVERT: O 15 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6064 (mt-10) REVERT: O 51 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7783 (mm-40) outliers start: 142 outliers final: 46 residues processed: 640 average time/residue: 1.6271 time to fit residues: 1296.3078 Evaluate side-chains 577 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 514 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 521 ARG Chi-restraints excluded: chain Q residue 354 GLU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 430 ASN Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 509 ARG Chi-restraints excluded: chain a residue 325 MET Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 7.9990 chunk 411 optimal weight: 7.9990 chunk 284 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 367 optimal weight: 4.9990 chunk 549 optimal weight: 3.9990 chunk 581 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 520 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 11 GLN H 80 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN P 390 ASN P 415 GLN S 324 ASN X 322 GLN b 390 ASN c 322 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 47066 Z= 0.197 Angle : 0.486 11.325 63704 Z= 0.259 Chirality : 0.042 0.173 7251 Planarity : 0.004 0.050 8400 Dihedral : 4.046 71.615 6857 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.72 % Allowed : 17.33 % Favored : 79.96 % 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: 2.09 (0.11), residues: 6048 helix: 2.79 (0.10), residues: 2548 sheet: 0.88 (0.14), residues: 1526 loop : -0.05 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.005 0.001 HIS X 365 PHE 0.032 0.002 PHE M 71 TYR 0.012 0.001 TYR C 143 ARG 0.010 0.000 ARG E 14 *********************** 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 659 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 533 time to evaluate : 5.118 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7060 (mp0) REVERT: C 132 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6271 (mt-10) REVERT: D 113 GLU cc_start: 0.6317 (mt-10) cc_final: 0.6001 (mp0) REVERT: E 13 MET cc_start: 0.6151 (mmm) cc_final: 0.5003 (mmp) REVERT: E 21 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.6256 (tmm160) REVERT: E 80 GLN cc_start: 0.8168 (tp40) cc_final: 0.7848 (tp40) REVERT: E 112 THR cc_start: 0.7028 (m) cc_final: 0.6772 (t) REVERT: E 113 GLU cc_start: 0.5760 (tt0) cc_final: 0.5263 (mm-30) REVERT: E 114 GLN cc_start: 0.5880 (OUTLIER) cc_final: 0.5413 (mm110) REVERT: E 121 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: E 135 ARG cc_start: 0.7090 (ptm160) cc_final: 0.6747 (ptm160) REVERT: E 163 ILE cc_start: 0.6247 (mp) cc_final: 0.6026 (mp) REVERT: E 165 ASN cc_start: 0.5667 (m-40) cc_final: 0.5388 (m-40) REVERT: F 29 SER cc_start: 0.6870 (m) cc_final: 0.6496 (p) REVERT: F 70 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: F 80 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: G 97 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7064 (ttm170) REVERT: G 176 SER cc_start: 0.7465 (m) cc_final: 0.7018 (p) REVERT: H 33 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7313 (pp) REVERT: H 152 HIS cc_start: 0.7414 (m90) cc_final: 0.6534 (m90) REVERT: I 159 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.5659 (t) REVERT: K 168 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7346 (mttt) REVERT: K 203 LEU cc_start: 0.6580 (mp) cc_final: 0.5707 (mt) REVERT: M 105 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8156 (mp-120) REVERT: M 149 ASP cc_start: 0.7689 (t0) cc_final: 0.7442 (t0) REVERT: N 13 MET cc_start: 0.7557 (tpp) cc_final: 0.6449 (mpp) REVERT: N 14 ARG cc_start: 0.6719 (ttp-110) cc_final: 0.6402 (ttp80) REVERT: N 21 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7086 (ttm-80) REVERT: P 330 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8096 (p0) REVERT: P 521 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7785 (mpt-90) REVERT: Q 354 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: R 325 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8045 (ttt) REVERT: S 361 VAL cc_start: 0.8982 (t) cc_final: 0.8733 (t) REVERT: T 339 ASP cc_start: 0.8091 (m-30) cc_final: 0.7829 (m-30) REVERT: U 395 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6426 (mpt) REVERT: U 401 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8214 (tt) REVERT: U 430 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8045 (t0) REVERT: V 461 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7602 (t0) REVERT: W 325 MET cc_start: 0.8223 (tmt) cc_final: 0.7929 (tmm) REVERT: W 509 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6993 (ttp-170) REVERT: X 512 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: Y 398 LEU cc_start: 0.8258 (mt) cc_final: 0.8039 (mt) REVERT: a 325 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7746 (tmm) REVERT: a 340 TYR cc_start: 0.8896 (m-80) cc_final: 0.8684 (m-80) REVERT: O 15 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6052 (mt-10) REVERT: O 51 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7782 (mm-40) outliers start: 126 outliers final: 54 residues processed: 609 average time/residue: 1.5382 time to fit residues: 1168.5199 Evaluate side-chains 591 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 514 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain P residue 521 ARG Chi-restraints excluded: chain Q residue 354 GLU Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain U residue 430 ASN Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain a residue 325 MET Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 496 optimal weight: 5.9990 chunk 402 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 0.0980 chunk 522 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN F 51 GLN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN K 216 ASN L 165 ASN M 105 GLN N 45 ASN N 80 GLN N 152 HIS P 322 GLN P 390 ASN P 415 GLN R 390 ASN S 324 ASN U 381 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN c 322 GLN h 172 GLN O 80 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 47066 Z= 0.356 Angle : 0.568 12.158 63704 Z= 0.301 Chirality : 0.045 0.254 7251 Planarity : 0.004 0.050 8400 Dihedral : 4.348 69.130 6857 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 16.90 % Favored : 79.53 % 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: 1.88 (0.11), residues: 6048 helix: 2.57 (0.10), residues: 2534 sheet: 0.84 (0.13), residues: 1526 loop : -0.13 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP c 429 HIS 0.006 0.001 HIS b 410 PHE 0.036 0.003 PHE M 71 TYR 0.014 0.002 TYR C 143 ARG 0.009 0.000 ARG E 14 *********************** 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 706 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 540 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8082 (mm-40) REVERT: A 156 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7629 (mtm) REVERT: A 161 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7053 (mp0) REVERT: C 126 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: C 132 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6340 (mt-10) REVERT: D 13 MET cc_start: 0.6320 (tpp) cc_final: 0.5523 (tmm) REVERT: D 135 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6442 (ttp80) REVERT: E 13 MET cc_start: 0.6184 (mmm) cc_final: 0.5035 (mmt) REVERT: E 80 GLN cc_start: 0.8193 (tp40) cc_final: 0.7867 (tp40) REVERT: E 112 THR cc_start: 0.7154 (m) cc_final: 0.6845 (t) REVERT: E 113 GLU cc_start: 0.5803 (tt0) cc_final: 0.5335 (mm-30) REVERT: E 114 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5654 (mm110) REVERT: E 165 ASN cc_start: 0.5683 (m-40) cc_final: 0.5399 (m-40) REVERT: F 70 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: F 80 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: G 14 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6716 (mmm-85) REVERT: G 97 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6997 (ttm170) REVERT: G 176 SER cc_start: 0.7594 (m) cc_final: 0.7024 (p) REVERT: H 156 MET cc_start: 0.7688 (mtm) cc_final: 0.7378 (mtm) REVERT: I 13 MET cc_start: 0.6697 (mmm) cc_final: 0.6400 (mmt) REVERT: I 70 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: I 153 PHE cc_start: 0.6863 (p90) cc_final: 0.6407 (p90) REVERT: I 159 THR cc_start: 0.6537 (OUTLIER) cc_final: 0.6135 (p) REVERT: M 80 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: M 105 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8206 (mm110) REVERT: M 137 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: M 149 ASP cc_start: 0.7697 (t0) cc_final: 0.7435 (t0) REVERT: N 14 ARG cc_start: 0.6843 (ttp-110) cc_final: 0.6447 (ttp80) REVERT: N 21 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.7116 (ttm-80) REVERT: N 168 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7363 (tptp) REVERT: P 330 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8134 (p0) REVERT: Q 519 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: R 325 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8081 (ttt) REVERT: S 361 VAL cc_start: 0.9115 (t) cc_final: 0.8827 (t) REVERT: T 430 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7755 (m110) REVERT: T 509 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6728 (tpt-90) REVERT: U 395 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6546 (mpt) REVERT: U 401 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8184 (tt) REVERT: V 461 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7519 (t0) REVERT: W 325 MET cc_start: 0.8234 (tmt) cc_final: 0.7933 (tmm) REVERT: W 509 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6935 (ttp-110) REVERT: X 512 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: Y 398 LEU cc_start: 0.8451 (mt) cc_final: 0.8238 (mt) REVERT: Z 447 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8528 (mtmp) REVERT: Z 507 GLU cc_start: 0.7570 (tp30) cc_final: 0.7358 (tp30) REVERT: O 15 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6042 (mt-10) REVERT: O 51 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7780 (mm-40) outliers start: 166 outliers final: 78 residues processed: 647 average time/residue: 1.4802 time to fit residues: 1179.1755 Evaluate side-chains 625 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 520 time to evaluate : 5.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 135 ARG Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 137 GLU Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 321 THR Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 313 VAL Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain V residue 433 GLU Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 355 PHE Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 322 GLN Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 339 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 401 LEU Chi-restraints excluded: chain Y residue 431 ILE Chi-restraints excluded: chain Y residue 503 VAL Chi-restraints excluded: chain Z residue 325 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 399 LEU Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 447 LYS Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 322 GLN Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 51 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.8980 chunk 524 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 582 optimal weight: 4.9990 chunk 483 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 322 GLN P 415 GLN S 324 ASN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47066 Z= 0.195 Angle : 0.489 11.544 63704 Z= 0.261 Chirality : 0.043 0.172 7251 Planarity : 0.004 0.047 8400 Dihedral : 4.085 65.317 6857 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.82 % Allowed : 18.47 % Favored : 78.71 % 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: 2.06 (0.11), residues: 6048 helix: 2.78 (0.10), residues: 2548 sheet: 0.87 (0.13), residues: 1526 loop : -0.10 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.004 0.001 HIS X 365 PHE 0.032 0.002 PHE M 71 TYR 0.016 0.001 TYR C 143 ARG 0.011 0.000 ARG E 14 *********************** 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 688 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 557 time to evaluate : 5.448 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7010 (mp0) REVERT: C 126 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: C 132 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6345 (mt-10) REVERT: D 13 MET cc_start: 0.6364 (tpp) cc_final: 0.5541 (tmm) REVERT: D 52 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7514 (mtpm) REVERT: E 13 MET cc_start: 0.6075 (mmm) cc_final: 0.4973 (mmp) REVERT: E 80 GLN cc_start: 0.8177 (tp40) cc_final: 0.7828 (tp-100) REVERT: E 112 THR cc_start: 0.7111 (m) cc_final: 0.6825 (t) REVERT: E 113 GLU cc_start: 0.5752 (tt0) cc_final: 0.5269 (mm-30) REVERT: E 114 GLN cc_start: 0.5947 (OUTLIER) cc_final: 0.5561 (mm110) REVERT: E 135 ARG cc_start: 0.7101 (ptm160) cc_final: 0.6835 (ptm160) REVERT: E 165 ASN cc_start: 0.5679 (m-40) cc_final: 0.5436 (m-40) REVERT: F 29 SER cc_start: 0.6859 (m) cc_final: 0.6439 (t) REVERT: F 70 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: F 80 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: G 14 ARG cc_start: 0.6842 (mmm-85) cc_final: 0.6632 (mmm-85) REVERT: G 73 ASN cc_start: 0.7523 (m110) cc_final: 0.7286 (m110) REVERT: G 97 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7005 (ttm170) REVERT: G 119 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: G 176 SER cc_start: 0.7593 (m) cc_final: 0.7039 (p) REVERT: H 33 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7354 (pp) REVERT: H 156 MET cc_start: 0.7682 (mtm) cc_final: 0.7450 (mtm) REVERT: I 13 MET cc_start: 0.6491 (mmm) cc_final: 0.6161 (mmt) REVERT: I 70 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: I 80 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8061 (tp40) REVERT: I 159 THR cc_start: 0.6486 (p) cc_final: 0.6090 (p) REVERT: K 168 LYS cc_start: 0.7934 (mtpp) cc_final: 0.7314 (mttt) REVERT: K 203 LEU cc_start: 0.6742 (mp) cc_final: 0.5797 (mt) REVERT: M 80 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: M 105 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8249 (mm110) REVERT: M 149 ASP cc_start: 0.7657 (t0) cc_final: 0.7398 (t0) REVERT: N 13 MET cc_start: 0.7536 (tpp) cc_final: 0.6541 (mpp) REVERT: N 14 ARG cc_start: 0.6862 (ttp-110) cc_final: 0.6561 (ttp80) REVERT: N 21 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.7118 (ttm-80) REVERT: P 330 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8077 (p0) REVERT: Q 519 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: R 325 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8047 (ttt) REVERT: R 339 ASP cc_start: 0.8431 (t0) cc_final: 0.8101 (t0) REVERT: S 361 VAL cc_start: 0.8997 (t) cc_final: 0.8742 (t) REVERT: T 430 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7781 (m110) REVERT: T 509 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6694 (tpt-90) REVERT: U 395 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6549 (mpt) REVERT: U 401 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8207 (tt) REVERT: U 430 ASN cc_start: 0.8397 (t0) cc_final: 0.8091 (t0) REVERT: V 461 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7483 (t0) REVERT: W 325 MET cc_start: 0.8227 (tmt) cc_final: 0.7930 (tmm) REVERT: W 509 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6929 (ttp-110) REVERT: X 512 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: Y 398 LEU cc_start: 0.8341 (mt) cc_final: 0.8119 (mt) REVERT: Z 507 GLU cc_start: 0.7554 (tp30) cc_final: 0.7342 (tp30) REVERT: O 15 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6155 (mt-10) REVERT: O 135 ARG cc_start: 0.7537 (ttt-90) cc_final: 0.7203 (ttt-90) outliers start: 131 outliers final: 62 residues processed: 638 average time/residue: 1.3818 time to fit residues: 1094.7836 Evaluate side-chains 617 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 531 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 52 LYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 168 LYS Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain N residue 114 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 401 LEU Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain T residue 430 ASN Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 354 GLU Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 401 LEU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Z residue 399 LEU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 447 LYS Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 343 THR Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 0.0020 chunk 65 optimal weight: 30.0000 chunk 331 optimal weight: 7.9990 chunk 425 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 chunk 490 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 580 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 267 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 216 ASN C 73 ASN D 51 GLN F 45 ASN F 51 GLN H 45 ASN H 80 GLN J 165 ASN K 216 ASN L 101 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 322 GLN P 390 ASN P 415 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 381 ASN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 47066 Z= 0.133 Angle : 0.459 10.949 63704 Z= 0.245 Chirality : 0.042 0.182 7251 Planarity : 0.003 0.048 8400 Dihedral : 3.842 60.687 6857 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.24 % Allowed : 19.31 % Favored : 78.45 % 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: 3.08 (0.10), residues: 2534 sheet: 0.91 (0.14), residues: 1526 loop : 0.01 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.004 0.001 HIS Q 365 PHE 0.031 0.002 PHE C 71 TYR 0.017 0.001 TYR C 143 ARG 0.013 0.000 ARG A 135 *********************** 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 679 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 575 time to evaluate : 4.097 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7064 (mp0) REVERT: C 126 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: C 132 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6352 (mt-10) REVERT: D 13 MET cc_start: 0.6304 (tpp) cc_final: 0.5489 (tmm) REVERT: E 13 MET cc_start: 0.5972 (mmm) cc_final: 0.4913 (mmp) REVERT: E 80 GLN cc_start: 0.8161 (tp40) cc_final: 0.7815 (tp-100) REVERT: E 112 THR cc_start: 0.6844 (m) cc_final: 0.6610 (t) REVERT: E 113 GLU cc_start: 0.5814 (tt0) cc_final: 0.5351 (mm-30) REVERT: E 114 GLN cc_start: 0.5924 (OUTLIER) cc_final: 0.5497 (mm110) REVERT: E 135 ARG cc_start: 0.7077 (ptm160) cc_final: 0.6823 (ptm160) REVERT: E 165 ASN cc_start: 0.5652 (m-40) cc_final: 0.5435 (m-40) REVERT: F 29 SER cc_start: 0.6875 (m) cc_final: 0.6500 (t) REVERT: G 14 ARG cc_start: 0.6826 (mmm-85) cc_final: 0.6606 (mmm-85) REVERT: G 73 ASN cc_start: 0.7486 (m110) cc_final: 0.7261 (m110) REVERT: G 169 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5281 (tp30) REVERT: G 176 SER cc_start: 0.7432 (m) cc_final: 0.6984 (p) REVERT: H 33 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7345 (pp) REVERT: H 152 HIS cc_start: 0.7426 (m90) cc_final: 0.6566 (m90) REVERT: I 70 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6978 (mm-30) REVERT: I 80 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (tp40) REVERT: I 159 THR cc_start: 0.6419 (p) cc_final: 0.6003 (p) REVERT: K 48 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7013 (mmp-170) REVERT: K 168 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7300 (mttt) REVERT: K 203 LEU cc_start: 0.6608 (mp) cc_final: 0.5682 (mt) REVERT: L 233 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7757 (tt) REVERT: M 105 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7906 (mp-120) REVERT: M 149 ASP cc_start: 0.7663 (t0) cc_final: 0.7424 (t0) REVERT: N 13 MET cc_start: 0.7548 (tpp) cc_final: 0.6479 (mpp) REVERT: N 14 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6565 (ttp80) REVERT: N 21 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.7090 (ttm-80) REVERT: P 330 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8042 (p0) REVERT: Q 395 MET cc_start: 0.7162 (tpp) cc_final: 0.6627 (tpt) REVERT: Q 519 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: R 325 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8075 (ttt) REVERT: R 339 ASP cc_start: 0.8395 (t0) cc_final: 0.8044 (t0) REVERT: S 361 VAL cc_start: 0.8963 (t) cc_final: 0.8712 (t) REVERT: S 509 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7134 (ttt180) REVERT: T 509 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6639 (tpt-90) REVERT: U 395 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6580 (mpt) REVERT: U 430 ASN cc_start: 0.8372 (t0) cc_final: 0.8078 (t0) REVERT: V 461 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7492 (t0) REVERT: W 325 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7907 (tmm) REVERT: W 430 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7942 (t0) REVERT: W 509 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6927 (ttp-110) REVERT: X 512 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: Y 395 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6043 (mpt) REVERT: Z 432 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: Z 507 GLU cc_start: 0.7519 (tp30) cc_final: 0.7308 (tp30) REVERT: b 325 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7599 (mpp) REVERT: b 354 GLU cc_start: 0.7896 (tt0) cc_final: 0.7251 (pt0) REVERT: O 15 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6213 (mt-10) outliers start: 104 outliers final: 49 residues processed: 635 average time/residue: 1.3105 time to fit residues: 1026.2396 Evaluate side-chains 605 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 532 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 147 ILE Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 44 GLU Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 368 optimal weight: 0.9990 chunk 395 optimal weight: 0.7980 chunk 286 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 456 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 45 ASN H 80 GLN J 11 GLN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 322 GLN P 390 ASN P 415 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 396 GLN Z 322 GLN b 390 ASN c 322 GLN O 80 GLN O 231 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 47066 Z= 0.148 Angle : 0.470 10.996 63704 Z= 0.249 Chirality : 0.042 0.167 7251 Planarity : 0.003 0.056 8400 Dihedral : 3.790 57.061 6856 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.16 % Allowed : 19.83 % Favored : 78.02 % 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: 2.37 (0.11), residues: 6048 helix: 3.14 (0.10), residues: 2534 sheet: 0.92 (0.14), residues: 1526 loop : 0.02 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.004 0.001 HIS X 365 PHE 0.030 0.002 PHE C 71 TYR 0.016 0.001 TYR C 143 ARG 0.013 0.000 ARG A 135 *********************** 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 643 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 543 time to evaluate : 4.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7062 (mp0) REVERT: C 126 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: C 132 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: D 13 MET cc_start: 0.6209 (tpp) cc_final: 0.5493 (tmm) REVERT: D 21 ARG cc_start: 0.6444 (mtt90) cc_final: 0.6199 (mmt-90) REVERT: E 13 MET cc_start: 0.5976 (mmm) cc_final: 0.4949 (mmt) REVERT: E 80 GLN cc_start: 0.8167 (tp40) cc_final: 0.7799 (tp-100) REVERT: E 112 THR cc_start: 0.6777 (m) cc_final: 0.6554 (t) REVERT: E 113 GLU cc_start: 0.5773 (tt0) cc_final: 0.5316 (mm-30) REVERT: E 114 GLN cc_start: 0.5801 (OUTLIER) cc_final: 0.5413 (mm110) REVERT: E 165 ASN cc_start: 0.5644 (m-40) cc_final: 0.5430 (m110) REVERT: E 219 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.7982 (ttp-110) REVERT: F 29 SER cc_start: 0.6930 (m) cc_final: 0.6528 (t) REVERT: G 14 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6580 (mmm-85) REVERT: G 73 ASN cc_start: 0.7470 (m110) cc_final: 0.7244 (m110) REVERT: G 119 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: G 169 GLU cc_start: 0.6472 (mm-30) cc_final: 0.5274 (tp30) REVERT: G 176 SER cc_start: 0.7407 (m) cc_final: 0.7014 (p) REVERT: G 233 LEU cc_start: 0.7299 (mp) cc_final: 0.6973 (tp) REVERT: H 33 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7359 (pp) REVERT: H 152 HIS cc_start: 0.7447 (m90) cc_final: 0.6617 (m90) REVERT: I 13 MET cc_start: 0.6695 (mmm) cc_final: 0.6171 (ttm) REVERT: I 70 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: I 80 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8042 (tp40) REVERT: I 159 THR cc_start: 0.6460 (p) cc_final: 0.6034 (p) REVERT: K 48 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6962 (mmp-170) REVERT: K 168 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7360 (mttt) REVERT: K 203 LEU cc_start: 0.6548 (mp) cc_final: 0.5640 (mt) REVERT: L 233 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7726 (tt) REVERT: M 105 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8201 (mm110) REVERT: M 149 ASP cc_start: 0.7668 (t0) cc_final: 0.7415 (t0) REVERT: N 13 MET cc_start: 0.7560 (tpp) cc_final: 0.6497 (mpp) REVERT: N 14 ARG cc_start: 0.6887 (ttp-110) cc_final: 0.6580 (ttp80) REVERT: N 21 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.7111 (ttm-80) REVERT: P 330 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8040 (p0) REVERT: Q 519 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: R 325 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (ttt) REVERT: R 339 ASP cc_start: 0.8401 (t0) cc_final: 0.8046 (t0) REVERT: S 361 VAL cc_start: 0.8979 (t) cc_final: 0.8727 (t) REVERT: S 509 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7065 (ttt180) REVERT: T 509 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6648 (tpt-90) REVERT: U 395 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6610 (mpt) REVERT: U 430 ASN cc_start: 0.8365 (t0) cc_final: 0.8066 (t0) REVERT: U 434 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: V 461 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7483 (t0) REVERT: W 325 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7904 (tmm) REVERT: W 430 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7953 (t0) REVERT: W 509 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6923 (ttp-110) REVERT: X 512 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: Y 395 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.5994 (mpt) REVERT: Z 432 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7060 (tp30) REVERT: Z 507 GLU cc_start: 0.7535 (tp30) cc_final: 0.7318 (tp30) REVERT: a 339 ASP cc_start: 0.8048 (p0) cc_final: 0.7819 (t70) REVERT: b 325 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7610 (mpp) REVERT: b 354 GLU cc_start: 0.7893 (tt0) cc_final: 0.7247 (pt0) REVERT: O 15 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6259 (mt-10) outliers start: 100 outliers final: 52 residues processed: 606 average time/residue: 1.3069 time to fit residues: 974.7703 Evaluate side-chains 604 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 526 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 0.9990 chunk 555 optimal weight: 0.1980 chunk 507 optimal weight: 3.9990 chunk 540 optimal weight: 0.6980 chunk 325 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 424 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 488 optimal weight: 7.9990 chunk 511 optimal weight: 6.9990 chunk 538 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN F 45 ASN H 45 ASN H 80 GLN J 11 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 390 ASN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 381 ASN Z 322 GLN b 390 ASN c 322 GLN d 172 GLN O 80 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2929 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= 0.140 Angle : 0.468 10.926 63704 Z= 0.248 Chirality : 0.042 0.176 7251 Planarity : 0.003 0.059 8400 Dihedral : 3.718 52.271 6856 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.00 % Allowed : 19.89 % Favored : 78.10 % 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: 2.43 (0.11), residues: 6048 helix: 3.20 (0.10), residues: 2534 sheet: 0.93 (0.14), residues: 1526 loop : 0.05 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 429 HIS 0.004 0.001 HIS Q 365 PHE 0.031 0.002 PHE C 71 TYR 0.016 0.001 TYR C 143 ARG 0.015 0.000 ARG A 135 *********************** 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 643 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 550 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.6927 (tp30) cc_final: 0.6715 (tp30) REVERT: A 51 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8079 (mm-40) REVERT: A 161 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7066 (mp0) REVERT: C 126 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: C 132 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6388 (mt-10) REVERT: D 13 MET cc_start: 0.6211 (tpp) cc_final: 0.5491 (tmm) REVERT: D 21 ARG cc_start: 0.6431 (mtt90) cc_final: 0.6179 (mtt90) REVERT: E 13 MET cc_start: 0.5968 (mmm) cc_final: 0.4934 (mmt) REVERT: E 22 LYS cc_start: 0.7501 (mtpt) cc_final: 0.6745 (ptpp) REVERT: E 80 GLN cc_start: 0.8162 (tp40) cc_final: 0.7796 (tp-100) REVERT: E 112 THR cc_start: 0.6714 (m) cc_final: 0.6510 (t) REVERT: E 113 GLU cc_start: 0.5745 (tt0) cc_final: 0.5276 (mm-30) REVERT: E 114 GLN cc_start: 0.5769 (OUTLIER) cc_final: 0.5375 (mm110) REVERT: E 135 ARG cc_start: 0.7006 (ptm160) cc_final: 0.6722 (ptm160) REVERT: E 165 ASN cc_start: 0.5654 (m-40) cc_final: 0.5438 (m110) REVERT: E 219 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.7985 (ttp-110) REVERT: F 29 SER cc_start: 0.6930 (m) cc_final: 0.6545 (t) REVERT: G 73 ASN cc_start: 0.7489 (m110) cc_final: 0.7258 (m110) REVERT: G 119 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: G 169 GLU cc_start: 0.6521 (mm-30) cc_final: 0.5321 (tp30) REVERT: G 176 SER cc_start: 0.7395 (m) cc_final: 0.6992 (p) REVERT: G 233 LEU cc_start: 0.7260 (mp) cc_final: 0.6956 (tp) REVERT: H 152 HIS cc_start: 0.7408 (m90) cc_final: 0.6598 (m90) REVERT: I 13 MET cc_start: 0.6543 (mmm) cc_final: 0.6100 (ttm) REVERT: I 22 LYS cc_start: 0.6637 (mtmt) cc_final: 0.5837 (mmmt) REVERT: I 70 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: I 80 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: I 159 THR cc_start: 0.6332 (p) cc_final: 0.5924 (p) REVERT: J 14 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6767 (ttp-110) REVERT: K 48 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6960 (mmp-170) REVERT: K 168 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7357 (mttt) REVERT: K 203 LEU cc_start: 0.6496 (mp) cc_final: 0.5633 (mt) REVERT: L 233 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7712 (tt) REVERT: M 105 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8215 (mm110) REVERT: M 149 ASP cc_start: 0.7657 (t0) cc_final: 0.7410 (t0) REVERT: N 13 MET cc_start: 0.7559 (tpp) cc_final: 0.6424 (mpp) REVERT: N 14 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6547 (ttp80) REVERT: N 21 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.7098 (ttm-80) REVERT: P 330 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (p0) REVERT: Q 519 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: R 325 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (ttt) REVERT: R 339 ASP cc_start: 0.8416 (t0) cc_final: 0.8074 (t0) REVERT: R 415 GLN cc_start: 0.7193 (mm110) cc_final: 0.6913 (tp40) REVERT: S 361 VAL cc_start: 0.8983 (t) cc_final: 0.8736 (t) REVERT: S 509 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7061 (ttt180) REVERT: T 509 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6636 (tpt-90) REVERT: U 395 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6507 (mpt) REVERT: U 430 ASN cc_start: 0.8357 (t0) cc_final: 0.8095 (t0) REVERT: U 434 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: V 461 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7469 (t0) REVERT: W 325 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (tmm) REVERT: W 430 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7925 (t0) REVERT: W 509 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6901 (ttp-170) REVERT: X 512 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: Y 395 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5977 (mpt) REVERT: Z 432 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: Z 507 GLU cc_start: 0.7538 (tp30) cc_final: 0.7280 (tp30) REVERT: b 325 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7548 (mpp) REVERT: b 354 GLU cc_start: 0.7861 (tt0) cc_final: 0.7203 (pt0) REVERT: O 15 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6195 (mt-10) outliers start: 93 outliers final: 53 residues processed: 603 average time/residue: 1.2700 time to fit residues: 945.8263 Evaluate side-chains 608 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 529 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 5.9990 chunk 571 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 397 optimal weight: 3.9990 chunk 599 optimal weight: 6.9990 chunk 551 optimal weight: 2.9990 chunk 477 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 368 optimal weight: 0.0570 chunk 292 optimal weight: 6.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN E 45 ASN F 45 ASN H 45 ASN H 80 GLN J 11 GLN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 390 ASN V 324 ASN Z 322 GLN c 322 GLN O 80 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 47066 Z= 0.211 Angle : 0.504 11.248 63704 Z= 0.266 Chirality : 0.043 0.180 7251 Planarity : 0.004 0.058 8400 Dihedral : 3.873 48.269 6856 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.96 % Allowed : 20.00 % Favored : 78.04 % 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: 3.07 (0.10), residues: 2534 sheet: 0.94 (0.14), residues: 1526 loop : 0.01 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 PHE 0.032 0.002 PHE M 71 TYR 0.017 0.001 TYR N 118 ARG 0.015 0.000 ARG A 135 ********************** 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 622 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 531 time to evaluate : 3.708 Fit side-chains REVERT: A 10 GLU cc_start: 0.6978 (tp30) cc_final: 0.6708 (tp30) REVERT: A 51 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: A 161 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7036 (mp0) REVERT: C 126 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: C 132 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: D 13 MET cc_start: 0.6272 (tpp) cc_final: 0.5497 (tmm) REVERT: E 13 MET cc_start: 0.5919 (mmm) cc_final: 0.4856 (mmp) REVERT: E 22 LYS cc_start: 0.7517 (mtpt) cc_final: 0.6730 (ptpp) REVERT: E 80 GLN cc_start: 0.8178 (tp40) cc_final: 0.7809 (tp-100) REVERT: E 112 THR cc_start: 0.6777 (m) cc_final: 0.6526 (t) REVERT: E 113 GLU cc_start: 0.5752 (tt0) cc_final: 0.5307 (mm-30) REVERT: E 114 GLN cc_start: 0.5805 (OUTLIER) cc_final: 0.5411 (mm110) REVERT: E 135 ARG cc_start: 0.7045 (ptm160) cc_final: 0.6738 (ptm160) REVERT: E 165 ASN cc_start: 0.5596 (m-40) cc_final: 0.5352 (m110) REVERT: F 29 SER cc_start: 0.7001 (m) cc_final: 0.6585 (t) REVERT: G 73 ASN cc_start: 0.7518 (m110) cc_final: 0.7287 (m110) REVERT: G 119 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: G 169 GLU cc_start: 0.6390 (mm-30) cc_final: 0.4884 (tp30) REVERT: G 176 SER cc_start: 0.7404 (m) cc_final: 0.7021 (p) REVERT: G 233 LEU cc_start: 0.7261 (mp) cc_final: 0.6974 (tp) REVERT: H 21 ARG cc_start: 0.6472 (mpp80) cc_final: 0.6217 (mtt180) REVERT: H 152 HIS cc_start: 0.7423 (m90) cc_final: 0.6547 (m90) REVERT: I 13 MET cc_start: 0.6563 (mmm) cc_final: 0.6110 (ttm) REVERT: I 22 LYS cc_start: 0.6588 (mtmt) cc_final: 0.6297 (pttt) REVERT: I 70 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: I 80 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (tp40) REVERT: I 159 THR cc_start: 0.6428 (p) cc_final: 0.5994 (p) REVERT: K 48 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6926 (mmp-170) REVERT: K 168 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7357 (mttt) REVERT: K 203 LEU cc_start: 0.6533 (mp) cc_final: 0.5691 (mt) REVERT: L 233 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7715 (tt) REVERT: M 105 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8188 (mm110) REVERT: M 149 ASP cc_start: 0.7682 (t0) cc_final: 0.7418 (t0) REVERT: N 13 MET cc_start: 0.7578 (tpp) cc_final: 0.6515 (mpp) REVERT: N 14 ARG cc_start: 0.6783 (ttp-110) cc_final: 0.6390 (ttp80) REVERT: N 21 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.7114 (ttm-80) REVERT: P 330 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.8064 (p0) REVERT: Q 519 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: R 325 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8084 (ttt) REVERT: R 339 ASP cc_start: 0.8423 (t0) cc_final: 0.8056 (t0) REVERT: R 415 GLN cc_start: 0.7183 (mm110) cc_final: 0.6951 (tp40) REVERT: S 361 VAL cc_start: 0.9043 (t) cc_final: 0.8782 (t) REVERT: S 509 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7136 (ttt180) REVERT: T 509 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6644 (tpt-90) REVERT: U 395 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6561 (mpt) REVERT: U 430 ASN cc_start: 0.8347 (t0) cc_final: 0.8086 (t0) REVERT: U 434 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: V 461 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7491 (t0) REVERT: W 325 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7917 (tmm) REVERT: W 430 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7949 (t0) REVERT: W 509 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6930 (ttp-170) REVERT: X 512 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: Y 395 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6022 (mpt) REVERT: Z 432 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: Z 507 GLU cc_start: 0.7566 (tp30) cc_final: 0.7349 (tp30) REVERT: b 325 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7597 (mpp) REVERT: b 354 GLU cc_start: 0.7925 (tt0) cc_final: 0.7267 (pt0) REVERT: O 15 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6115 (mt-10) REVERT: O 135 ARG cc_start: 0.7570 (ttt-90) cc_final: 0.7180 (ttt-90) outliers start: 91 outliers final: 55 residues processed: 587 average time/residue: 1.2299 time to fit residues: 897.2027 Evaluate side-chains 601 residues out of total 4641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 520 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 51 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain P residue 301 THR Chi-restraints excluded: chain P residue 330 ASP Chi-restraints excluded: chain P residue 354 GLU Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 519 GLU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain S residue 313 VAL Chi-restraints excluded: chain S residue 351 VAL Chi-restraints excluded: chain S residue 401 LEU Chi-restraints excluded: chain S residue 503 VAL Chi-restraints excluded: chain S residue 509 ARG Chi-restraints excluded: chain T residue 509 ARG Chi-restraints excluded: chain U residue 325 MET Chi-restraints excluded: chain U residue 355 PHE Chi-restraints excluded: chain U residue 395 MET Chi-restraints excluded: chain U residue 434 GLU Chi-restraints excluded: chain V residue 301 THR Chi-restraints excluded: chain V residue 461 ASP Chi-restraints excluded: chain W residue 301 THR Chi-restraints excluded: chain W residue 325 MET Chi-restraints excluded: chain W residue 401 LEU Chi-restraints excluded: chain W residue 430 ASN Chi-restraints excluded: chain W residue 509 ARG Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 401 LEU Chi-restraints excluded: chain X residue 409 ILE Chi-restraints excluded: chain X residue 512 GLU Chi-restraints excluded: chain Y residue 313 VAL Chi-restraints excluded: chain Y residue 325 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 348 THR Chi-restraints excluded: chain Y residue 355 PHE Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 432 GLU Chi-restraints excluded: chain a residue 401 LEU Chi-restraints excluded: chain a residue 412 SER Chi-restraints excluded: chain a residue 430 ASN Chi-restraints excluded: chain a residue 507 GLU Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 351 VAL Chi-restraints excluded: chain c residue 364 GLU Chi-restraints excluded: chain c residue 500 ASP Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 0.3980 chunk 508 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 440 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 478 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 491 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 73 ASN D 51 GLN E 45 ASN F 45 ASN H 45 ASN H 80 GLN I 101 ASN J 11 GLN J 165 ASN K 216 ASN L 165 ASN M 105 GLN M 216 ASN N 45 ASN N 80 GLN N 152 HIS P 322 GLN P 390 ASN V 324 ASN Z 322 GLN c 322 GLN O 80 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090528 restraints weight = 56531.637| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.65 r_work: 0.2809 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 47066 Z= 0.197 Angle : 0.499 11.329 63704 Z= 0.264 Chirality : 0.043 0.207 7251 Planarity : 0.004 0.061 8400 Dihedral : 3.866 45.165 6856 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.00 % Allowed : 20.17 % Favored : 77.82 % 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: 2.31 (0.11), residues: 6048 helix: 3.05 (0.10), residues: 2534 sheet: 0.93 (0.14), residues: 1526 loop : 0.01 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 429 HIS 0.004 0.001 HIS Y 365 PHE 0.032 0.002 PHE M 71 TYR 0.017 0.001 TYR C 143 ARG 0.016 0.000 ARG E 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15753.38 seconds wall clock time: 276 minutes 19.33 seconds (16579.33 seconds total)