Starting phenix.real_space_refine on Tue Mar 3 22:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.map" model { file = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2026/6wtd_21894.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 50 5.16 5 C 6110 2.51 5 N 1419 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9139 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 534 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 526 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 522 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1750 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 393 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 52} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 520 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 63} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 522 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 2.27, per 1000 atoms: 0.25 Number of scatterers: 9139 At special positions: 0 Unit cell: (97.96, 114.08, 116.56, 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 50 16.00 O 1560 8.00 N 1419 7.00 C 6110 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: 0.63 Conformation dependent library (CDL) restraints added in 339.5 milliseconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'K' and resid 2 through 13 removed outlier: 3.928A pdb=" N ALA K 6 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY K 11 " --> pdb=" O ALA K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 18 removed outlier: 3.606A pdb=" N ILE K 17 " --> pdb=" O ILE K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 37 removed outlier: 3.927A pdb=" N ILE K 26 " --> pdb=" O ALA K 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE K 28 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 43 through 57 removed outlier: 3.763A pdb=" N PHE K 48 " --> pdb=" O LYS K 44 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 3.652A pdb=" N GLY K 54 " --> pdb=" O MET K 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 57 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 63 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 71 through 74 removed outlier: 3.846A pdb=" N PHE K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 74' Processing helix chain 'L' and resid 7 through 15 removed outlier: 3.927A pdb=" N GLY L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA L 12 " --> pdb=" O LYS L 8 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY L 13 " --> pdb=" O TYR L 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE L 14 " --> pdb=" O ILE L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 40 removed outlier: 3.613A pdb=" N ILE L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN L 35 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN L 40 " --> pdb=" O GLY L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 48 Processing helix chain 'L' and resid 51 through 56 Processing helix chain 'L' and resid 59 through 64 removed outlier: 3.573A pdb=" N LEU L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 59 through 64' Processing helix chain 'L' and resid 68 through 72 removed outlier: 4.459A pdb=" N LEU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 12 Processing helix chain 'M' and resid 20 through 40 removed outlier: 3.942A pdb=" N ILE M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 39 " --> pdb=" O ASN M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 59 removed outlier: 3.710A pdb=" N MET M 50 " --> pdb=" O THR M 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 65 through 70 Processing helix chain 'N' and resid 4 through 6 No H-bonds generated for 'chain 'N' and resid 4 through 6' Processing helix chain 'N' and resid 7 through 14 removed outlier: 4.093A pdb=" N GLY N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY N 13 " --> pdb=" O TYR N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 20 removed outlier: 3.733A pdb=" N GLY N 18 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU N 19 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 26 removed outlier: 3.598A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 37 removed outlier: 3.810A pdb=" N ASN N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 42 No H-bonds generated for 'chain 'N' and resid 40 through 42' Processing helix chain 'N' and resid 43 through 66 Proline residue: N 49 - end of helix removed outlier: 3.596A pdb=" N ILE N 52 " --> pdb=" O PHE N 48 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU N 53 " --> pdb=" O PRO N 49 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY N 54 " --> pdb=" O MET N 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 10 removed outlier: 3.522A pdb=" N LYS O 8 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR O 9 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 18 removed outlier: 3.599A pdb=" N THR O 16 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE O 17 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY O 18 " --> pdb=" O SER O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 13 through 18' Processing helix chain 'O' and resid 26 through 37 removed outlier: 4.009A pdb=" N PHE O 30 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 42 No H-bonds generated for 'chain 'O' and resid 40 through 42' Processing helix chain 'O' and resid 43 through 48 removed outlier: 3.595A pdb=" N VAL O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE O 48 " --> pdb=" O LYS O 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 43 through 48' Processing helix chain 'O' and resid 51 through 59 removed outlier: 3.675A pdb=" N ALA O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU O 57 " --> pdb=" O LEU O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 65 removed outlier: 3.521A pdb=" N CYS O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 71 Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.699A pdb=" N TYR P 9 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA P 12 " --> pdb=" O LYS P 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER P 15 " --> pdb=" O GLY P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 19 through 32 removed outlier: 3.548A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 40 removed outlier: 3.523A pdb=" N ARG P 39 " --> pdb=" O ASN P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 64 removed outlier: 3.766A pdb=" N ILE P 52 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.647A pdb=" N VAL P 68 " --> pdb=" O CYS P 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 14 removed outlier: 3.991A pdb=" N GLY Q 13 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 40 removed outlier: 3.624A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE Q 30 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN Q 35 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER Q 38 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN Q 40 " --> pdb=" O GLY Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 removed outlier: 3.812A pdb=" N MET Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 71 Processing helix chain 'Q' and resid 72 through 74 No H-bonds generated for 'chain 'Q' and resid 72 through 74' Processing helix chain 'R' and resid 3 through 11 removed outlier: 3.700A pdb=" N TYR R 9 " --> pdb=" O LEU R 5 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 38 removed outlier: 4.475A pdb=" N ALA R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 44 removed outlier: 3.516A pdb=" N ILE R 43 " --> pdb=" O ASN R 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 40 through 44' Processing helix chain 'R' and resid 47 through 74 removed outlier: 3.647A pdb=" N ALA R 51 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY R 62 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.750A pdb=" N TYR S 9 " --> pdb=" O LEU S 5 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 26 removed outlier: 3.762A pdb=" N GLY S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 24 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 Processing helix chain 'S' and resid 33 through 40 Processing helix chain 'S' and resid 43 through 53 removed outlier: 3.700A pdb=" N PHE S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) Proline residue: S 49 - end of helix Processing helix chain 'S' and resid 53 through 62 removed outlier: 3.755A pdb=" N LEU S 57 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 70 removed outlier: 3.637A pdb=" N MET S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 14 removed outlier: 3.932A pdb=" N TYR T 9 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 18 removed outlier: 3.774A pdb=" N GLY T 18 " --> pdb=" O SER T 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 15 through 18' Processing helix chain 'T' and resid 19 through 24 Processing helix chain 'T' and resid 26 through 34 removed outlier: 3.647A pdb=" N PHE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 42 No H-bonds generated for 'chain 'T' and resid 40 through 42' Processing helix chain 'T' and resid 43 through 60 removed outlier: 3.737A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.501A pdb=" N LEU T 53 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU T 57 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA T 60 " --> pdb=" O ALA T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 65 removed outlier: 4.061A pdb=" N CYS T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 62 through 65' Processing helix chain 'T' and resid 66 through 74 removed outlier: 3.741A pdb=" N LEU T 72 " --> pdb=" O VAL T 68 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 14 removed outlier: 4.094A pdb=" N LEU 8 13 " --> pdb=" O PHE 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 17 through 29 removed outlier: 3.604A pdb=" N THR 8 22 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE 8 25 " --> pdb=" O ILE 8 21 " (cutoff:3.500A) Processing helix chain '8' and resid 33 through 45 removed outlier: 3.534A pdb=" N ARG 8 37 " --> pdb=" O PRO 8 33 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG 8 42 " --> pdb=" O LEU 8 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 32 through 42 removed outlier: 3.627A pdb=" N VAL X 36 " --> pdb=" O TYR X 32 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU X 37 " --> pdb=" O THR X 33 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE X 40 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 71 removed outlier: 4.095A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 76 removed outlier: 3.580A pdb=" N GLN X 76 " --> pdb=" O MET X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 92 Processing helix chain 'X' and resid 92 through 98 removed outlier: 3.807A pdb=" N ILE X 98 " --> pdb=" O MET X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 137 removed outlier: 4.168A pdb=" N ILE X 118 " --> pdb=" O HIS X 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE X 123 " --> pdb=" O ILE X 119 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL X 124 " --> pdb=" O SER X 120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN X 129 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR X 130 " --> pdb=" O TRP X 126 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR X 135 " --> pdb=" O ILE X 131 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 138 through 145 removed outlier: 3.904A pdb=" N PHE X 142 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU X 144 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 164 removed outlier: 3.553A pdb=" N LEU X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE X 160 " --> pdb=" O PRO X 156 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 181 removed outlier: 3.854A pdb=" N LEU X 173 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE X 181 " --> pdb=" O LEU X 177 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 185 Processing helix chain 'X' and resid 188 through 200 removed outlier: 3.597A pdb=" N GLY X 193 " --> pdb=" O VAL X 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU X 194 " --> pdb=" O ILE X 190 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN X 197 " --> pdb=" O GLY X 193 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU X 200 " --> pdb=" O PHE X 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 245 removed outlier: 3.817A pdb=" N LEU X 217 " --> pdb=" O LEU X 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU X 222 " --> pdb=" O ALA X 218 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU X 223 " --> pdb=" O ILE X 219 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE X 228 " --> pdb=" O PHE X 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY X 231 " --> pdb=" O GLY X 227 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR X 241 " --> pdb=" O LEU X 237 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU X 242 " --> pdb=" O THR X 238 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS X 243 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP X 244 " --> pdb=" O SER X 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 63 removed outlier: 3.972A pdb=" N PHE Z 62 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 72 removed outlier: 3.536A pdb=" N VAL Z 69 " --> pdb=" O PHE Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 103 removed outlier: 4.840A pdb=" N PHE Z 80 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA Z 83 " --> pdb=" O ASP Z 79 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG Z 84 " --> pdb=" O PHE Z 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN Z 93 " --> pdb=" O SER Z 89 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER Z 95 " --> pdb=" O VAL Z 91 " (cutoff:3.500A) Processing helix chain '7' and resid 117 through 126 removed outlier: 4.230A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 142 removed outlier: 3.595A pdb=" N THR 7 139 " --> pdb=" O VAL 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 143 through 155 removed outlier: 4.076A pdb=" N VAL 7 149 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 56 removed outlier: 4.562A pdb=" N TYR U 55 " --> pdb=" O TYR U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 83 removed outlier: 3.631A pdb=" N TRP U 67 " --> pdb=" O GLY U 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE U 69 " --> pdb=" O PRO U 65 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY U 72 " --> pdb=" O HIS U 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE U 73 " --> pdb=" O PHE U 69 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA U 75 " --> pdb=" O LEU U 71 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET U 80 " --> pdb=" O PHE U 76 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU U 81 " --> pdb=" O GLY U 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 27 Proline residue: J 15 - end of helix removed outlier: 3.869A pdb=" N ALA J 21 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1065 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: 1.17 Time building geometry restraints manager: 0.92 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: 2719 1.34 - 1.46: 2259 1.46 - 1.58: 4246 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9314 Sorted by residual: bond pdb=" SD FME P 1 " pdb=" CE FME P 1 " ideal model delta sigma weight residual 1.805 1.750 0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" SD FME K 1 " pdb=" CE FME K 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" CG FME P 1 " pdb=" SD FME P 1 " ideal model delta sigma weight residual 1.817 1.769 0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" N FME P 1 " pdb=" CN FME P 1 " ideal model delta sigma weight residual 1.335 1.381 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" N PRO X 212 " pdb=" CA PRO X 212 " ideal model delta sigma weight residual 1.468 1.485 -0.018 7.90e-03 1.60e+04 5.11e+00 ... (remaining 9309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11955 2.33 - 4.67: 559 4.67 - 7.00: 72 7.00 - 9.34: 26 9.34 - 11.67: 7 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C VAL X 211 " pdb=" N PRO X 212 " pdb=" CA PRO X 212 " ideal model delta sigma weight residual 121.65 113.94 7.71 1.01e+00 9.80e-01 5.82e+01 angle pdb=" N ILE N 17 " pdb=" CA ILE N 17 " pdb=" C ILE N 17 " ideal model delta sigma weight residual 113.47 106.44 7.03 1.01e+00 9.80e-01 4.84e+01 angle pdb=" N ILE N 26 " pdb=" CA ILE N 26 " pdb=" C ILE N 26 " ideal model delta sigma weight residual 112.29 106.42 5.87 9.40e-01 1.13e+00 3.91e+01 angle pdb=" N ILE X 98 " pdb=" CA ILE X 98 " pdb=" C ILE X 98 " ideal model delta sigma weight residual 111.91 106.75 5.16 8.90e-01 1.26e+00 3.36e+01 angle pdb=" C VAL L 47 " pdb=" N PHE L 48 " pdb=" CA PHE L 48 " ideal model delta sigma weight residual 120.06 126.20 -6.14 1.19e+00 7.06e-01 2.66e+01 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 4661 17.12 - 34.24: 586 34.24 - 51.37: 119 51.37 - 68.49: 10 68.49 - 85.61: 4 Dihedral angle restraints: 5380 sinusoidal: 1904 harmonic: 3476 Sorted by residual: dihedral pdb=" CA PHE T 64 " pdb=" C PHE T 64 " pdb=" N CYS T 65 " pdb=" CA CYS T 65 " ideal model delta harmonic sigma weight residual 180.00 142.03 37.97 0 5.00e+00 4.00e-02 5.77e+01 dihedral pdb=" CA LEU O 20 " pdb=" C LEU O 20 " pdb=" N GLY O 21 " pdb=" CA GLY O 21 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LEU S 19 " pdb=" C LEU S 19 " pdb=" N LEU S 20 " pdb=" CA LEU S 20 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1005 0.053 - 0.107: 437 0.107 - 0.160: 92 0.160 - 0.213: 19 0.213 - 0.267: 3 Chirality restraints: 1556 Sorted by residual: chirality pdb=" CB ILE T 43 " pdb=" CA ILE T 43 " pdb=" CG1 ILE T 43 " pdb=" CG2 ILE T 43 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE X 98 " pdb=" CA ILE X 98 " pdb=" CG1 ILE X 98 " pdb=" CG2 ILE X 98 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE M 14 " pdb=" CA ILE M 14 " pdb=" CG1 ILE M 14 " pdb=" CG2 ILE M 14 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1553 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 48 " 0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO L 49 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO L 49 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 49 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE N 48 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO N 49 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO N 49 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 49 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 48 " -0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO M 49 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO M 49 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 49 " -0.039 5.00e-02 4.00e+02 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1444 2.75 - 3.29: 8978 3.29 - 3.82: 15325 3.82 - 4.36: 17994 4.36 - 4.90: 28096 Nonbonded interactions: 71837 Sorted by model distance: nonbonded pdb=" OH TYR X 32 " pdb=" O PHE X 109 " model vdw 2.208 3.040 nonbonded pdb=" O ALA L 12 " pdb=" OG1 THR L 16 " model vdw 2.249 3.040 nonbonded pdb=" O LEU S 57 " pdb=" OG1 THR S 61 " model vdw 2.259 3.040 nonbonded pdb=" O ASN Z 53 " pdb=" OG SER Z 56 " model vdw 2.272 3.040 nonbonded pdb=" O VAL X 116 " pdb=" OG SER X 120 " model vdw 2.275 3.040 ... (remaining 71832 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 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 56 or (resi \ d 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throug \ h 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or re \ sid 62 through 63 or (resid 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 66 or (resid 67 and (name N or name CA or name C or \ name O or name CB )) or resid 68 through 74)) selection = (chain 'L' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 56 or (resid 57 and (n \ ame N or name CA or name C or name O or name CB )) or resid 58 through 60 or (re \ sid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 66 or (resid 67 and (name N or name CA or name C or name O or n \ ame CB )) or resid 68 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or re \ sid 58 through 63 or (resid 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 66 or (resid 67 and (name N or name CA or name C or \ name O or name CB )) or resid 68 through 74)) selection = (chain 'N' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or re \ sid 58 through 60 or (resid 61 and (name N or name CA or name C or name O or nam \ e CB )) or resid 62 through 63 or (resid 64 and (name N or name CA or name C or \ name O or name CB )) or resid 65 through 66 or (resid 67 and (name N or name CA \ or name C or name O or name CB )) or resid 68 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 41 or (resi \ d 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throug \ h 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or re \ sid 58 through 60 or (resid 61 and (name N or name CA or name C or name O or nam \ e CB )) or resid 62 through 63 or (resid 64 and (name N or name CA or name C or \ name O or name CB )) or resid 65 through 66 or (resid 67 and (name N or name CA \ or name C or name O or name CB )) or resid 68 through 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 63 or (re \ sid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thro \ ugh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 74)) selection = (chain 'Q' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 41 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 56 or (resid 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 63 or (re \ sid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thro \ ugh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 74)) selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 74)) selection = (chain 'S' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 41 or (resid 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 56 or (resid 57 and (n \ ame N or name CA or name C or name O or name CB )) or resid 58 through 60 or (re \ sid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 66 or (resid 67 and (name N or name CA or name C or name O or n \ ame CB )) or resid 68 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 through 25 or (resid 26 through \ 27 and (name N or name CA or name C or name O or name CB )) or resid 28 through \ 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or resi \ d 43 through 56 or (resid 57 and (name N or name CA or name C or name O or name \ CB )) or resid 58 through 60 or (resid 61 and (name N or name CA or name C or na \ me O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name CA or \ name C or name O or name CB )) or resid 65 through 66 or (resid 67 and (name N \ or name CA or name C or name O or name CB )) or resid 68 through 74)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.007 0.057 9314 Z= 0.342 Angle : 1.166 11.669 12619 Z= 0.629 Chirality : 0.060 0.267 1556 Planarity : 0.008 0.080 1533 Dihedral : 15.331 85.612 3156 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.86 % Allowed : 20.00 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.31 (0.16), residues: 1191 helix: -4.52 (0.08), residues: 803 sheet: None (None), residues: 0 loop : -2.83 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 57 TYR 0.016 0.002 TYR 8 39 PHE 0.032 0.003 PHE M 70 TRP 0.011 0.002 TRP J 14 HIS 0.007 0.002 HIS X 114 Details of bonding type rmsd covalent geometry : bond 0.00711 ( 9314) covalent geometry : angle 1.16630 (12619) hydrogen bonds : bond 0.31739 ( 366) hydrogen bonds : angle 11.30820 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 358 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 10 ILE cc_start: 0.9414 (pt) cc_final: 0.9160 (pt) REVERT: K 14 ILE cc_start: 0.8972 (tt) cc_final: 0.8754 (pt) REVERT: L 10 ILE cc_start: 0.8776 (tt) cc_final: 0.8306 (mp) REVERT: L 39 ARG cc_start: 0.4703 (tmt170) cc_final: 0.4373 (tmt170) REVERT: M 44 LYS cc_start: 0.7181 (ptpp) cc_final: 0.6904 (tmmt) REVERT: M 50 MET cc_start: 0.7656 (mmt) cc_final: 0.7333 (mmm) REVERT: M 55 PHE cc_start: 0.8058 (t80) cc_final: 0.7519 (t80) REVERT: N 9 TYR cc_start: 0.7439 (m-80) cc_final: 0.7203 (m-10) REVERT: N 28 ILE cc_start: 0.9065 (pt) cc_final: 0.8856 (tt) REVERT: N 47 VAL cc_start: 0.7241 (t) cc_final: 0.6888 (t) REVERT: N 59 GLU cc_start: 0.8256 (tt0) cc_final: 0.8009 (tt0) REVERT: P 39 ARG cc_start: 0.6987 (mmt180) cc_final: 0.6329 (tpm170) REVERT: P 48 PHE cc_start: 0.7898 (t80) cc_final: 0.7561 (t80) REVERT: R 50 MET cc_start: 0.7753 (ppp) cc_final: 0.7443 (ppp) REVERT: S 44 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8403 (tptm) REVERT: S 59 GLU cc_start: 0.8752 (pp20) cc_final: 0.8454 (pp20) REVERT: T 16 THR cc_start: 0.9079 (p) cc_final: 0.8607 (t) REVERT: 8 34 MET cc_start: 0.9278 (ppp) cc_final: 0.9003 (ppp) REVERT: 8 37 ARG cc_start: 0.9047 (mtp180) cc_final: 0.8811 (mtp85) REVERT: 8 39 TYR cc_start: 0.9055 (m-10) cc_final: 0.8629 (m-10) REVERT: X 85 TYR cc_start: 0.8224 (m-80) cc_final: 0.7977 (m-80) REVERT: X 199 MET cc_start: 0.5045 (tmm) cc_final: 0.3636 (tpp) REVERT: 7 150 GLU cc_start: 0.8716 (tp30) cc_final: 0.7934 (tp30) REVERT: U 48 LEU cc_start: 0.7745 (mp) cc_final: 0.7369 (mp) REVERT: J 9 ILE cc_start: 0.6632 (pt) cc_final: 0.6078 (mt) outliers start: 8 outliers final: 4 residues processed: 364 average time/residue: 0.0759 time to fit residues: 40.1534 Evaluate side-chains 271 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 2 GLN N 2 GLN ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.108118 restraints weight = 27322.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.110407 restraints weight = 17394.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112105 restraints weight = 12296.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113200 restraints weight = 9427.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114125 restraints weight = 7756.856| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9314 Z= 0.147 Angle : 0.750 8.782 12619 Z= 0.370 Chirality : 0.044 0.167 1556 Planarity : 0.005 0.051 1533 Dihedral : 6.184 28.972 1275 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.43 % Allowed : 7.35 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.19), residues: 1191 helix: -3.39 (0.13), residues: 830 sheet: None (None), residues: 0 loop : -2.62 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 39 TYR 0.013 0.002 TYR U 51 PHE 0.031 0.002 PHE J 17 TRP 0.013 0.002 TRP J 14 HIS 0.004 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9314) covalent geometry : angle 0.75034 (12619) hydrogen bonds : bond 0.05082 ( 366) hydrogen bonds : angle 6.16079 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7987 (tp) cc_final: 0.7753 (tp) REVERT: K 43 ILE cc_start: 0.9053 (tp) cc_final: 0.8747 (tp) REVERT: L 39 ARG cc_start: 0.4735 (tmt170) cc_final: 0.4500 (tmt170) REVERT: N 3 LEU cc_start: 0.6111 (pt) cc_final: 0.5907 (pt) REVERT: N 9 TYR cc_start: 0.7596 (m-80) cc_final: 0.7344 (m-10) REVERT: N 19 LEU cc_start: 0.7907 (pt) cc_final: 0.7504 (pp) REVERT: N 70 PHE cc_start: 0.7331 (m-80) cc_final: 0.7099 (m-80) REVERT: O 50 MET cc_start: 0.6970 (ptt) cc_final: 0.4918 (ttp) REVERT: P 48 PHE cc_start: 0.7774 (t80) cc_final: 0.7536 (t80) REVERT: P 67 MET cc_start: 0.8137 (mmm) cc_final: 0.7884 (tpp) REVERT: R 3 LEU cc_start: 0.8545 (tp) cc_final: 0.8263 (tp) REVERT: T 16 THR cc_start: 0.9166 (p) cc_final: 0.8590 (t) REVERT: 8 34 MET cc_start: 0.9134 (ppp) cc_final: 0.8709 (ppp) REVERT: X 58 TRP cc_start: 0.5110 (m-90) cc_final: 0.4466 (t-100) REVERT: X 63 GLU cc_start: 0.8797 (tt0) cc_final: 0.8328 (tm-30) REVERT: X 69 ILE cc_start: 0.8620 (mp) cc_final: 0.8246 (mp) REVERT: X 85 TYR cc_start: 0.8453 (m-80) cc_final: 0.8135 (m-80) REVERT: X 169 ARG cc_start: 0.7522 (ttm170) cc_final: 0.7307 (ttm110) REVERT: X 199 MET cc_start: 0.5060 (tmm) cc_final: 0.3670 (tpp) REVERT: 7 131 ASP cc_start: 0.7133 (m-30) cc_final: 0.6695 (m-30) REVERT: 7 150 GLU cc_start: 0.8828 (tp30) cc_final: 0.7689 (tp30) REVERT: 7 154 LYS cc_start: 0.8948 (mtmt) cc_final: 0.7887 (mtmm) REVERT: 7 169 ASN cc_start: 0.8301 (m-40) cc_final: 0.8100 (m-40) REVERT: U 48 LEU cc_start: 0.7798 (mp) cc_final: 0.7282 (mp) REVERT: J 9 ILE cc_start: 0.6302 (pt) cc_final: 0.5771 (mt) outliers start: 4 outliers final: 2 residues processed: 355 average time/residue: 0.0758 time to fit residues: 38.9768 Evaluate side-chains 275 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 40 ASN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110272 restraints weight = 27330.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112429 restraints weight = 17825.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113786 restraints weight = 12898.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.115048 restraints weight = 10204.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.115773 restraints weight = 8418.060| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9314 Z= 0.133 Angle : 0.703 8.568 12619 Z= 0.345 Chirality : 0.044 0.220 1556 Planarity : 0.004 0.035 1533 Dihedral : 5.652 27.341 1275 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.22), residues: 1191 helix: -2.68 (0.15), residues: 848 sheet: None (None), residues: 0 loop : -2.42 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 39 TYR 0.013 0.001 TYR U 31 PHE 0.022 0.001 PHE N 64 TRP 0.009 0.002 TRP U 67 HIS 0.009 0.001 HIS U 68 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9314) covalent geometry : angle 0.70301 (12619) hydrogen bonds : bond 0.04128 ( 366) hydrogen bonds : angle 5.39154 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 43 ILE cc_start: 0.9019 (tp) cc_final: 0.8699 (tp) REVERT: K 53 LEU cc_start: 0.8025 (tp) cc_final: 0.7776 (tp) REVERT: L 39 ARG cc_start: 0.4997 (tmt170) cc_final: 0.4774 (tmt170) REVERT: M 44 LYS cc_start: 0.7804 (tmmt) cc_final: 0.7365 (tmtt) REVERT: N 9 TYR cc_start: 0.7366 (m-80) cc_final: 0.7124 (m-10) REVERT: N 19 LEU cc_start: 0.7836 (pt) cc_final: 0.7501 (pp) REVERT: O 50 MET cc_start: 0.6666 (ptt) cc_final: 0.5047 (ttp) REVERT: P 67 MET cc_start: 0.7845 (mmm) cc_final: 0.7635 (tpp) REVERT: Q 63 LEU cc_start: 0.8117 (mm) cc_final: 0.7178 (pp) REVERT: R 10 ILE cc_start: 0.9222 (pt) cc_final: 0.9013 (pt) REVERT: S 44 LYS cc_start: 0.8819 (tmtt) cc_final: 0.8463 (tptt) REVERT: T 16 THR cc_start: 0.9112 (p) cc_final: 0.8564 (t) REVERT: T 45 ASP cc_start: 0.8380 (p0) cc_final: 0.8167 (p0) REVERT: T 67 MET cc_start: 0.7507 (ppp) cc_final: 0.7277 (ppp) REVERT: 8 34 MET cc_start: 0.9115 (ppp) cc_final: 0.8610 (ppp) REVERT: X 38 LEU cc_start: 0.8600 (tt) cc_final: 0.8219 (tp) REVERT: X 63 GLU cc_start: 0.8733 (tt0) cc_final: 0.8509 (tm-30) REVERT: X 85 TYR cc_start: 0.8406 (m-80) cc_final: 0.8149 (m-80) REVERT: X 199 MET cc_start: 0.5178 (tmm) cc_final: 0.4948 (tmm) REVERT: X 216 ILE cc_start: 0.9372 (mp) cc_final: 0.8904 (mp) REVERT: X 243 LYS cc_start: 0.8359 (tttp) cc_final: 0.8152 (tptt) REVERT: Z 93 ASN cc_start: 0.8310 (m110) cc_final: 0.8052 (t0) REVERT: 7 150 GLU cc_start: 0.8729 (tp30) cc_final: 0.8130 (tp30) REVERT: 7 154 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8238 (mtpp) REVERT: 7 169 ASN cc_start: 0.8188 (m-40) cc_final: 0.7842 (m-40) REVERT: 7 170 LEU cc_start: 0.8781 (mp) cc_final: 0.7657 (mp) REVERT: U 48 LEU cc_start: 0.7771 (mp) cc_final: 0.7347 (mp) REVERT: J 9 ILE cc_start: 0.6247 (pt) cc_final: 0.5687 (mt) REVERT: J 10 LEU cc_start: 0.8131 (mp) cc_final: 0.7838 (mt) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.0711 time to fit residues: 36.5894 Evaluate side-chains 283 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.0170 chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 114 HIS ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.128126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.112231 restraints weight = 27169.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114437 restraints weight = 17824.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115969 restraints weight = 12875.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116985 restraints weight = 10073.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.117822 restraints weight = 8418.171| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9314 Z= 0.126 Angle : 0.694 7.868 12619 Z= 0.332 Chirality : 0.043 0.279 1556 Planarity : 0.004 0.034 1533 Dihedral : 5.280 25.067 1275 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.23), residues: 1191 helix: -2.19 (0.16), residues: 839 sheet: None (None), residues: 0 loop : -2.45 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 39 TYR 0.014 0.001 TYR S 9 PHE 0.028 0.001 PHE Z 62 TRP 0.008 0.001 TRP J 14 HIS 0.002 0.001 HIS X 114 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9314) covalent geometry : angle 0.69435 (12619) hydrogen bonds : bond 0.03643 ( 366) hydrogen bonds : angle 4.85904 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 LEU cc_start: 0.3459 (mp) cc_final: 0.2547 (tt) REVERT: L 39 ARG cc_start: 0.5168 (tmt170) cc_final: 0.4849 (tmt170) REVERT: M 44 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7373 (tmtt) REVERT: N 9 TYR cc_start: 0.7350 (m-80) cc_final: 0.7086 (m-10) REVERT: P 39 ARG cc_start: 0.7044 (tpm170) cc_final: 0.6721 (tpm170) REVERT: P 67 MET cc_start: 0.7732 (mmm) cc_final: 0.7385 (tpp) REVERT: Q 63 LEU cc_start: 0.7940 (mm) cc_final: 0.7028 (pp) REVERT: R 59 GLU cc_start: 0.5749 (tt0) cc_final: 0.5488 (tt0) REVERT: S 44 LYS cc_start: 0.8780 (tmtt) cc_final: 0.8500 (tptt) REVERT: T 16 THR cc_start: 0.8971 (p) cc_final: 0.8436 (t) REVERT: T 45 ASP cc_start: 0.8277 (p0) cc_final: 0.8053 (p0) REVERT: T 67 MET cc_start: 0.7148 (ppp) cc_final: 0.6924 (ppp) REVERT: 8 34 MET cc_start: 0.9125 (ppp) cc_final: 0.8585 (ppp) REVERT: X 38 LEU cc_start: 0.8695 (tt) cc_final: 0.8333 (tp) REVERT: X 63 GLU cc_start: 0.8663 (tt0) cc_final: 0.8453 (tm-30) REVERT: X 85 TYR cc_start: 0.8424 (m-80) cc_final: 0.8130 (m-80) REVERT: X 216 ILE cc_start: 0.9401 (mp) cc_final: 0.9019 (mp) REVERT: Z 93 ASN cc_start: 0.8456 (m110) cc_final: 0.8216 (t0) REVERT: 7 132 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7499 (pt0) REVERT: 7 150 GLU cc_start: 0.8551 (tp30) cc_final: 0.8047 (tp30) REVERT: 7 154 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8166 (mtpp) REVERT: 7 169 ASN cc_start: 0.8511 (m-40) cc_final: 0.8263 (t0) REVERT: 7 170 LEU cc_start: 0.9048 (mp) cc_final: 0.7814 (mp) REVERT: U 48 LEU cc_start: 0.7782 (mp) cc_final: 0.7508 (mp) REVERT: J 9 ILE cc_start: 0.6472 (pt) cc_final: 0.5856 (mt) REVERT: J 10 LEU cc_start: 0.7952 (mp) cc_final: 0.7711 (mp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.0706 time to fit residues: 36.9273 Evaluate side-chains 289 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.125522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110448 restraints weight = 27837.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112352 restraints weight = 18164.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114898 restraints weight = 12517.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115125 restraints weight = 8896.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115235 restraints weight = 8184.378| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9314 Z= 0.140 Angle : 0.705 9.236 12619 Z= 0.342 Chirality : 0.044 0.174 1556 Planarity : 0.004 0.036 1533 Dihedral : 5.208 23.361 1275 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.24), residues: 1191 helix: -1.75 (0.17), residues: 827 sheet: None (None), residues: 0 loop : -2.14 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 7 128 TYR 0.012 0.001 TYR T 9 PHE 0.033 0.001 PHE K 64 TRP 0.008 0.001 TRP X 126 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9314) covalent geometry : angle 0.70486 (12619) hydrogen bonds : bond 0.03448 ( 366) hydrogen bonds : angle 4.77371 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 43 ILE cc_start: 0.9035 (tp) cc_final: 0.8824 (tp) REVERT: K 52 ILE cc_start: 0.8581 (mm) cc_final: 0.8287 (mm) REVERT: L 8 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8368 (tttp) REVERT: L 39 ARG cc_start: 0.5348 (tmt170) cc_final: 0.5000 (tmt170) REVERT: L 50 MET cc_start: 0.7177 (tmm) cc_final: 0.6950 (tpp) REVERT: M 44 LYS cc_start: 0.7829 (tmmt) cc_final: 0.7388 (tmtt) REVERT: N 9 TYR cc_start: 0.7333 (m-80) cc_final: 0.7095 (m-10) REVERT: O 50 MET cc_start: 0.6728 (ptt) cc_final: 0.4979 (ttp) REVERT: P 39 ARG cc_start: 0.6904 (tpm170) cc_final: 0.6687 (tpm170) REVERT: P 40 ASN cc_start: 0.7753 (t0) cc_final: 0.7552 (t0) REVERT: P 67 MET cc_start: 0.7652 (mmm) cc_final: 0.7337 (tpp) REVERT: Q 63 LEU cc_start: 0.7979 (mm) cc_final: 0.7105 (pp) REVERT: S 44 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8579 (tptt) REVERT: T 16 THR cc_start: 0.8857 (p) cc_final: 0.8350 (t) REVERT: 8 34 MET cc_start: 0.9112 (ppp) cc_final: 0.8627 (ppp) REVERT: X 38 LEU cc_start: 0.8717 (tt) cc_final: 0.8359 (tp) REVERT: X 63 GLU cc_start: 0.8648 (tt0) cc_final: 0.8354 (tt0) REVERT: X 85 TYR cc_start: 0.8390 (m-80) cc_final: 0.8088 (m-80) REVERT: X 236 ILE cc_start: 0.9401 (mm) cc_final: 0.9135 (mt) REVERT: Z 93 ASN cc_start: 0.8442 (m110) cc_final: 0.8205 (t0) REVERT: 7 132 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7526 (pt0) REVERT: 7 150 GLU cc_start: 0.8538 (tp30) cc_final: 0.8077 (tp30) REVERT: 7 154 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8463 (ttmm) REVERT: J 9 ILE cc_start: 0.6661 (pt) cc_final: 0.6004 (mt) REVERT: J 10 LEU cc_start: 0.8034 (mp) cc_final: 0.7730 (mt) REVERT: J 23 VAL cc_start: 0.9482 (t) cc_final: 0.9258 (t) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.0709 time to fit residues: 36.8133 Evaluate side-chains 290 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 50 optimal weight: 0.0870 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 29 GLN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.125398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109576 restraints weight = 28303.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111705 restraints weight = 18627.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113175 restraints weight = 13534.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.114156 restraints weight = 10669.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.115053 restraints weight = 8971.408| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9314 Z= 0.145 Angle : 0.714 9.572 12619 Z= 0.344 Chirality : 0.044 0.148 1556 Planarity : 0.004 0.033 1533 Dihedral : 5.185 23.506 1275 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.24), residues: 1191 helix: -1.55 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -1.90 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 84 TYR 0.018 0.001 TYR X 232 PHE 0.024 0.002 PHE Z 62 TRP 0.008 0.001 TRP X 126 HIS 0.001 0.000 HIS U 68 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9314) covalent geometry : angle 0.71444 (12619) hydrogen bonds : bond 0.03408 ( 366) hydrogen bonds : angle 4.75567 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 8 LYS cc_start: 0.8675 (tttt) cc_final: 0.7194 (tptt) REVERT: K 20 LEU cc_start: 0.7739 (tp) cc_final: 0.7206 (tp) REVERT: K 43 ILE cc_start: 0.9078 (tp) cc_final: 0.8847 (tp) REVERT: K 52 ILE cc_start: 0.8495 (mm) cc_final: 0.8229 (mm) REVERT: L 16 THR cc_start: 0.8384 (m) cc_final: 0.8129 (t) REVERT: L 39 ARG cc_start: 0.5457 (tmt170) cc_final: 0.5090 (tmt170) REVERT: M 44 LYS cc_start: 0.7801 (tmmt) cc_final: 0.7352 (tmtt) REVERT: N 9 TYR cc_start: 0.7328 (m-80) cc_final: 0.7098 (m-10) REVERT: N 40 ASN cc_start: 0.8655 (t0) cc_final: 0.8312 (t0) REVERT: O 50 MET cc_start: 0.6586 (ptt) cc_final: 0.4837 (ttp) REVERT: P 67 MET cc_start: 0.7602 (mmm) cc_final: 0.7285 (tpp) REVERT: Q 61 THR cc_start: 0.8143 (t) cc_final: 0.7793 (m) REVERT: Q 63 LEU cc_start: 0.7917 (mm) cc_final: 0.7078 (pp) REVERT: T 16 THR cc_start: 0.8910 (p) cc_final: 0.8381 (t) REVERT: 8 34 MET cc_start: 0.9126 (ppp) cc_final: 0.8811 (ppp) REVERT: X 38 LEU cc_start: 0.8714 (tt) cc_final: 0.8374 (tp) REVERT: X 63 GLU cc_start: 0.8632 (tt0) cc_final: 0.8314 (tt0) REVERT: X 85 TYR cc_start: 0.8448 (m-80) cc_final: 0.8208 (m-80) REVERT: Z 93 ASN cc_start: 0.8628 (m110) cc_final: 0.8239 (t0) REVERT: 7 132 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7501 (pt0) REVERT: 7 150 GLU cc_start: 0.8570 (tp30) cc_final: 0.8074 (tp30) REVERT: 7 154 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8259 (mtpp) REVERT: 7 164 LYS cc_start: 0.8754 (mmpt) cc_final: 0.8540 (mmmt) REVERT: U 79 SER cc_start: 0.8186 (m) cc_final: 0.7752 (p) REVERT: J 2 LEU cc_start: 0.7629 (mt) cc_final: 0.7409 (mt) REVERT: J 9 ILE cc_start: 0.6720 (pt) cc_final: 0.6042 (mt) REVERT: J 10 LEU cc_start: 0.8098 (mp) cc_final: 0.7855 (mt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.0701 time to fit residues: 35.7968 Evaluate side-chains 294 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 2 GLN 7 169 ASN ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.128040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112403 restraints weight = 28316.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114500 restraints weight = 18733.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116027 restraints weight = 13722.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.117005 restraints weight = 10776.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.117821 restraints weight = 9044.298| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9314 Z= 0.119 Angle : 0.716 9.805 12619 Z= 0.336 Chirality : 0.043 0.211 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.025 22.249 1275 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.11 % Allowed : 2.05 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.25), residues: 1191 helix: -1.32 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 84 TYR 0.016 0.001 TYR T 9 PHE 0.030 0.002 PHE K 64 TRP 0.010 0.001 TRP X 126 HIS 0.002 0.001 HIS U 29 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9314) covalent geometry : angle 0.71587 (12619) hydrogen bonds : bond 0.03274 ( 366) hydrogen bonds : angle 4.52355 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7679 (tp) cc_final: 0.7475 (tp) REVERT: K 43 ILE cc_start: 0.9093 (tp) cc_final: 0.8809 (tp) REVERT: K 52 ILE cc_start: 0.8349 (mm) cc_final: 0.8074 (mm) REVERT: L 39 ARG cc_start: 0.5142 (tmt170) cc_final: 0.4931 (tmt170) REVERT: M 44 LYS cc_start: 0.7846 (tmmt) cc_final: 0.7454 (tmtt) REVERT: N 9 TYR cc_start: 0.7290 (m-80) cc_final: 0.7038 (m-10) REVERT: N 19 LEU cc_start: 0.7735 (pt) cc_final: 0.7489 (pp) REVERT: N 40 ASN cc_start: 0.8665 (t0) cc_final: 0.8204 (t0) REVERT: N 52 ILE cc_start: 0.7770 (mt) cc_final: 0.7416 (mm) REVERT: O 34 ILE cc_start: 0.7871 (mt) cc_final: 0.7473 (mt) REVERT: O 50 MET cc_start: 0.6528 (ptt) cc_final: 0.4723 (ttp) REVERT: P 39 ARG cc_start: 0.6696 (tpm170) cc_final: 0.6435 (tpm170) REVERT: P 40 ASN cc_start: 0.7729 (t0) cc_final: 0.7518 (t0) REVERT: P 67 MET cc_start: 0.7620 (mmm) cc_final: 0.7105 (tpp) REVERT: Q 35 ASN cc_start: 0.8454 (p0) cc_final: 0.7669 (t0) REVERT: Q 61 THR cc_start: 0.8279 (t) cc_final: 0.7956 (m) REVERT: Q 63 LEU cc_start: 0.7720 (mm) cc_final: 0.7097 (pp) REVERT: R 59 GLU cc_start: 0.5844 (tt0) cc_final: 0.5614 (tt0) REVERT: S 44 LYS cc_start: 0.8704 (tmtt) cc_final: 0.8466 (tptt) REVERT: S 67 MET cc_start: 0.8189 (tpt) cc_final: 0.7945 (tpt) REVERT: T 16 THR cc_start: 0.8897 (p) cc_final: 0.8381 (t) REVERT: 8 15 TYR cc_start: 0.5627 (m-80) cc_final: 0.5420 (m-80) REVERT: 8 34 MET cc_start: 0.9118 (ppp) cc_final: 0.8767 (ppp) REVERT: X 38 LEU cc_start: 0.8693 (tt) cc_final: 0.8345 (tp) REVERT: X 85 TYR cc_start: 0.8427 (m-80) cc_final: 0.8113 (m-80) REVERT: Z 93 ASN cc_start: 0.8627 (m110) cc_final: 0.8289 (t0) REVERT: 7 132 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7478 (pt0) REVERT: 7 150 GLU cc_start: 0.8535 (tp30) cc_final: 0.8093 (tp30) REVERT: 7 152 MET cc_start: 0.7931 (ptp) cc_final: 0.7298 (ptp) REVERT: 7 154 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8319 (mtpp) REVERT: 7 170 LEU cc_start: 0.8739 (mp) cc_final: 0.6761 (mp) REVERT: 7 171 ASN cc_start: 0.8375 (p0) cc_final: 0.8060 (p0) REVERT: J 9 ILE cc_start: 0.6537 (pt) cc_final: 0.6003 (mt) REVERT: J 10 LEU cc_start: 0.8051 (mp) cc_final: 0.7838 (mt) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.0679 time to fit residues: 35.5768 Evaluate side-chains 300 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 29 GLN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.112295 restraints weight = 28086.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114428 restraints weight = 18564.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.115626 restraints weight = 13483.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116963 restraints weight = 10816.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.117663 restraints weight = 8960.410| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9314 Z= 0.129 Angle : 0.737 10.360 12619 Z= 0.347 Chirality : 0.044 0.197 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.049 23.692 1275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.25), residues: 1191 helix: -1.14 (0.18), residues: 811 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 128 TYR 0.022 0.001 TYR X 232 PHE 0.019 0.001 PHE X 95 TRP 0.008 0.001 TRP X 82 HIS 0.001 0.000 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9314) covalent geometry : angle 0.73697 (12619) hydrogen bonds : bond 0.03181 ( 366) hydrogen bonds : angle 4.47917 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7721 (tp) cc_final: 0.7414 (tp) REVERT: K 52 ILE cc_start: 0.8245 (mm) cc_final: 0.7967 (mm) REVERT: L 39 ARG cc_start: 0.5267 (tmt170) cc_final: 0.4796 (tmt170) REVERT: M 44 LYS cc_start: 0.7892 (tmmt) cc_final: 0.7418 (tmtt) REVERT: N 9 TYR cc_start: 0.7300 (m-80) cc_final: 0.7015 (m-10) REVERT: N 19 LEU cc_start: 0.7789 (pt) cc_final: 0.7584 (pp) REVERT: N 40 ASN cc_start: 0.8672 (t0) cc_final: 0.8243 (t0) REVERT: N 52 ILE cc_start: 0.7775 (mt) cc_final: 0.7492 (mm) REVERT: O 50 MET cc_start: 0.6284 (ptt) cc_final: 0.4460 (ttp) REVERT: P 39 ARG cc_start: 0.6521 (tpm170) cc_final: 0.6296 (tpm170) REVERT: P 40 ASN cc_start: 0.7793 (t0) cc_final: 0.7586 (t0) REVERT: P 67 MET cc_start: 0.7669 (mmm) cc_final: 0.7136 (tpp) REVERT: Q 35 ASN cc_start: 0.8424 (p0) cc_final: 0.7654 (t0) REVERT: Q 61 THR cc_start: 0.8201 (t) cc_final: 0.7924 (m) REVERT: Q 63 LEU cc_start: 0.7752 (mm) cc_final: 0.7099 (pp) REVERT: R 59 GLU cc_start: 0.5886 (tt0) cc_final: 0.5637 (tt0) REVERT: T 16 THR cc_start: 0.8864 (p) cc_final: 0.8336 (t) REVERT: 8 34 MET cc_start: 0.9138 (ppp) cc_final: 0.8807 (ppp) REVERT: X 38 LEU cc_start: 0.8692 (tt) cc_final: 0.8362 (tp) REVERT: X 85 TYR cc_start: 0.8427 (m-80) cc_final: 0.8174 (m-80) REVERT: Z 93 ASN cc_start: 0.8622 (m110) cc_final: 0.8307 (t0) REVERT: 7 132 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7554 (pt0) REVERT: 7 140 LYS cc_start: 0.8862 (tptt) cc_final: 0.8656 (mtmm) REVERT: 7 154 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8597 (mtpp) REVERT: J 9 ILE cc_start: 0.6757 (pt) cc_final: 0.6143 (mt) REVERT: J 10 LEU cc_start: 0.8087 (mp) cc_final: 0.7877 (mt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.0685 time to fit residues: 35.3218 Evaluate side-chains 298 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 2 GLN L 40 ASN ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.124268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108507 restraints weight = 28726.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110618 restraints weight = 18870.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111917 restraints weight = 13716.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113138 restraints weight = 10926.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113816 restraints weight = 9037.859| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9314 Z= 0.179 Angle : 0.775 9.810 12619 Z= 0.373 Chirality : 0.046 0.187 1556 Planarity : 0.004 0.033 1533 Dihedral : 5.302 22.907 1275 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.25), residues: 1191 helix: -1.25 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -1.66 (0.37), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 84 TYR 0.020 0.001 TYR J 25 PHE 0.029 0.002 PHE K 64 TRP 0.014 0.001 TRP X 82 HIS 0.002 0.001 HIS X 137 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9314) covalent geometry : angle 0.77548 (12619) hydrogen bonds : bond 0.03363 ( 366) hydrogen bonds : angle 4.73965 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7761 (tp) cc_final: 0.7529 (tp) REVERT: M 44 LYS cc_start: 0.7880 (tmmt) cc_final: 0.7648 (tmmt) REVERT: N 9 TYR cc_start: 0.7317 (m-80) cc_final: 0.7032 (m-10) REVERT: N 40 ASN cc_start: 0.8693 (t0) cc_final: 0.8269 (t0) REVERT: O 50 MET cc_start: 0.6488 (ptt) cc_final: 0.5571 (ptm) REVERT: Q 61 THR cc_start: 0.8218 (t) cc_final: 0.7865 (m) REVERT: Q 63 LEU cc_start: 0.7916 (mm) cc_final: 0.7177 (pp) REVERT: S 67 MET cc_start: 0.8136 (tpt) cc_final: 0.7820 (tpt) REVERT: T 16 THR cc_start: 0.8816 (p) cc_final: 0.8370 (t) REVERT: 8 34 MET cc_start: 0.9166 (ppp) cc_final: 0.8848 (ppp) REVERT: X 38 LEU cc_start: 0.8736 (tt) cc_final: 0.8365 (tp) REVERT: Z 93 ASN cc_start: 0.8679 (m110) cc_final: 0.8300 (t0) REVERT: 7 150 GLU cc_start: 0.8556 (tp30) cc_final: 0.8349 (tm-30) REVERT: 7 152 MET cc_start: 0.7955 (ptp) cc_final: 0.7483 (ptp) REVERT: 7 154 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8503 (ttpt) REVERT: 7 157 LYS cc_start: 0.8874 (tmmt) cc_final: 0.8425 (ttpt) REVERT: J 9 ILE cc_start: 0.6735 (pt) cc_final: 0.6309 (mt) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.0654 time to fit residues: 32.2691 Evaluate side-chains 278 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.0000 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.127770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111755 restraints weight = 28429.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.113910 restraints weight = 18936.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115314 restraints weight = 13801.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.116453 restraints weight = 10968.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117065 restraints weight = 9133.051| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9314 Z= 0.125 Angle : 0.767 10.244 12619 Z= 0.355 Chirality : 0.043 0.150 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.072 23.840 1275 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.25), residues: 1191 helix: -1.09 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.44 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 84 TYR 0.030 0.001 TYR X 85 PHE 0.022 0.001 PHE U 76 TRP 0.013 0.001 TRP X 82 HIS 0.001 0.000 HIS X 185 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9314) covalent geometry : angle 0.76737 (12619) hydrogen bonds : bond 0.03223 ( 366) hydrogen bonds : angle 4.56236 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7629 (tp) cc_final: 0.7414 (tp) REVERT: K 52 ILE cc_start: 0.8180 (mm) cc_final: 0.7898 (mm) REVERT: M 44 LYS cc_start: 0.7850 (tmmt) cc_final: 0.7354 (tmtt) REVERT: N 9 TYR cc_start: 0.7276 (m-80) cc_final: 0.7023 (m-10) REVERT: N 19 LEU cc_start: 0.8142 (pt) cc_final: 0.7917 (pp) REVERT: N 40 ASN cc_start: 0.8681 (t0) cc_final: 0.8260 (t0) REVERT: N 52 ILE cc_start: 0.7654 (mt) cc_final: 0.7394 (mm) REVERT: P 67 MET cc_start: 0.7295 (mmm) cc_final: 0.6997 (tpp) REVERT: Q 35 ASN cc_start: 0.8405 (p0) cc_final: 0.7686 (t0) REVERT: Q 61 THR cc_start: 0.8185 (t) cc_final: 0.7909 (m) REVERT: Q 63 LEU cc_start: 0.7818 (mm) cc_final: 0.7226 (pp) REVERT: R 47 VAL cc_start: 0.8812 (m) cc_final: 0.8406 (p) REVERT: T 16 THR cc_start: 0.8765 (p) cc_final: 0.8238 (t) REVERT: 8 34 MET cc_start: 0.9126 (ppp) cc_final: 0.8808 (ppp) REVERT: X 38 LEU cc_start: 0.8728 (tt) cc_final: 0.8379 (tp) REVERT: X 74 LYS cc_start: 0.8972 (tppt) cc_final: 0.8490 (tptt) REVERT: Z 90 ASP cc_start: 0.7914 (p0) cc_final: 0.7453 (m-30) REVERT: Z 93 ASN cc_start: 0.8602 (m110) cc_final: 0.8282 (t0) REVERT: 7 132 GLU cc_start: 0.8512 (tp30) cc_final: 0.8050 (pt0) REVERT: 7 140 LYS cc_start: 0.8868 (tptt) cc_final: 0.8663 (mtmm) REVERT: 7 154 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8458 (ttpt) REVERT: J 9 ILE cc_start: 0.6509 (pt) cc_final: 0.6237 (mt) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.0659 time to fit residues: 33.6984 Evaluate side-chains 299 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.129869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.113943 restraints weight = 27726.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.116055 restraints weight = 18527.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.117492 restraints weight = 13599.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.118681 restraints weight = 10853.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.119394 restraints weight = 9035.228| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9314 Z= 0.123 Angle : 0.773 10.789 12619 Z= 0.352 Chirality : 0.043 0.149 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.048 35.455 1275 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.25), residues: 1191 helix: -0.93 (0.19), residues: 818 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 128 TYR 0.022 0.001 TYR J 25 PHE 0.017 0.001 PHE Z 62 TRP 0.010 0.001 TRP J 14 HIS 0.001 0.000 HIS X 185 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9314) covalent geometry : angle 0.77259 (12619) hydrogen bonds : bond 0.03133 ( 366) hydrogen bonds : angle 4.44556 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.00 seconds wall clock time: 25 minutes 34.64 seconds (1534.64 seconds total)