Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:32:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_21894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_21894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_21894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_21894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtd_21894/12_2022/6wtd_21894_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 45": "OD1" <-> "OD2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 45": "OD1" <-> "OD2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "X PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 59": "OD1" <-> "OD2" Residue "U PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 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: 5.63, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 71 helices and 0 sheets defined 66.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'K' and resid 3 through 12 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 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 20 through 36 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 41 through 56 removed outlier: 3.912A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL K 47 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 3.650A pdb=" N ILE K 52 " --> pdb=" O PRO K 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA K 56 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 No H-bonds generated for 'chain 'K' and resid 59 through 62' Processing helix chain 'K' and resid 65 through 69 Processing helix chain 'K' and resid 71 through 73 No H-bonds generated for 'chain 'K' and resid 71 through 73' Processing helix chain 'L' and resid 8 through 39 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) removed outlier: 4.064A pdb=" N THR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY L 18 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) 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) Processing helix chain 'L' and resid 43 through 47 removed outlier: 3.585A pdb=" N VAL L 47 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 55 No H-bonds generated for 'chain 'L' and resid 52 through 55' Processing helix chain 'L' and resid 60 through 63 No H-bonds generated for 'chain 'L' and resid 60 through 63' Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.570A pdb=" N GLY M 13 " --> pdb=" O TYR M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 39 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 47 through 61 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) removed outlier: 3.873A pdb=" N ALA M 60 " --> pdb=" O ALA M 56 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 69 removed outlier: 3.853A pdb=" N VAL M 68 " --> pdb=" O CYS M 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 13 removed outlier: 3.743A pdb=" N LYS N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR N 9 " --> pdb=" O ALA N 6 " (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 22 through 25 No H-bonds generated for 'chain 'N' and resid 22 through 25' Processing helix chain 'N' and resid 28 through 36 removed outlier: 3.810A pdb=" N ASN N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 65 removed outlier: 6.500A pdb=" N ASP N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 46 " --> pdb=" O ILE N 43 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE N 48 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.802A pdb=" N ILE N 52 " --> pdb=" O PRO N 49 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU N 53 " --> pdb=" O MET N 50 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU N 57 " --> pdb=" O GLY N 54 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER N 58 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU N 59 " --> pdb=" O ALA N 56 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR N 61 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU N 63 " --> pdb=" O ALA N 60 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE N 64 " --> pdb=" O THR N 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 70 No H-bonds generated for 'chain 'N' and resid 67 through 70' Processing helix chain 'O' and resid 5 through 9 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) No H-bonds generated for 'chain 'O' and resid 5 through 9' Processing helix chain 'O' and resid 14 through 17 removed outlier: 3.869A pdb=" N ILE O 17 " --> pdb=" O ILE O 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 26 through 36 removed outlier: 4.009A pdb=" N PHE O 30 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 64 removed outlier: 3.871A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL O 47 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix removed outlier: 5.732A pdb=" N ILE O 52 " --> pdb=" O PRO O 49 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU O 53 " --> pdb=" O MET O 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA O 56 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA O 60 " --> pdb=" O LEU O 57 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU O 63 " --> pdb=" O ALA O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 4.239A pdb=" N LEU O 72 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 31 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) removed outlier: 4.157A pdb=" N THR P 16 " --> pdb=" O ALA P 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY P 18 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) 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 34 through 39 removed outlier: 3.523A pdb=" N ARG P 39 " --> pdb=" O ASN P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 63 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 66 through 68 No H-bonds generated for 'chain 'P' and resid 66 through 68' Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.910A pdb=" N LYS Q 8 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR Q 9 " --> pdb=" O LEU Q 5 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 20 No H-bonds generated for 'chain 'Q' and resid 18 through 20' Processing helix chain 'Q' and resid 23 through 39 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) Processing helix chain 'Q' and resid 47 through 62 removed outlier: 3.956A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 73 removed outlier: 3.822A pdb=" N VAL Q 68 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER Q 69 " --> pdb=" O CYS Q 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU Q 72 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU Q 73 " --> pdb=" O SER Q 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 7 No H-bonds generated for 'chain 'R' and resid 4 through 7' Processing helix chain 'R' and resid 17 through 37 removed outlier: 3.818A pdb=" N GLY R 21 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY R 25 " --> pdb=" O ALA R 22 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE R 26 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE R 28 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL R 29 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE R 34 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN R 35 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 37 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 43 No H-bonds generated for 'chain 'R' and resid 41 through 43' Processing helix chain 'R' and resid 48 through 73 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 39 removed outlier: 4.128A pdb=" N TYR S 9 " --> pdb=" O ALA S 6 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE S 10 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY S 11 " --> pdb=" O LYS S 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY S 13 " --> pdb=" O ILE S 10 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR S 16 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE S 17 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY S 18 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU S 19 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY S 21 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE S 24 " --> pdb=" O GLY S 21 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY S 25 " --> pdb=" O ALA S 22 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE S 28 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL S 29 " --> pdb=" O ILE S 26 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA S 31 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA S 32 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE S 34 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN S 35 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER S 38 " --> pdb=" O ASN S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 52 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 54 through 61 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 64 through 71 removed outlier: 3.946A pdb=" N LEU S 71 " --> pdb=" O MET S 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 23 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) removed outlier: 4.306A pdb=" N SER T 15 " --> pdb=" O GLY T 11 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR T 16 " --> pdb=" O ALA T 12 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY T 18 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 33 Processing helix chain 'T' and resid 41 through 59 removed outlier: 5.895A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR T 46 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL T 47 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.997A pdb=" N ILE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU T 53 " --> pdb=" O MET T 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA T 56 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU T 57 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU T 59 " --> pdb=" O ALA T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 73 removed outlier: 4.115A pdb=" N MET T 67 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL T 68 " --> pdb=" O CYS T 65 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU T 71 " --> pdb=" O VAL T 68 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 16 removed outlier: 4.094A pdb=" N LEU 8 13 " --> pdb=" O PHE 8 9 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR 8 15 " --> pdb=" O ASN 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 28 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 34 through 44 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 33 through 41 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 57 through 75 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) removed outlier: 4.578A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 91 Processing helix chain 'X' and resid 93 through 104 removed outlier: 3.807A pdb=" N ILE X 98 " --> pdb=" O MET X 94 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA X 99 " --> pdb=" O PHE X 95 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU X 101 " --> pdb=" O PHE X 97 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE X 102 " --> pdb=" O ILE X 98 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER X 103 " --> pdb=" O ALA X 99 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 136 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 144 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) Processing helix chain 'X' and resid 152 through 165 Proline residue: X 156 - end of helix 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) removed outlier: 3.839A pdb=" N SER X 165 " --> pdb=" O ILE X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 180 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) Processing helix chain 'X' and resid 182 through 186 Processing helix chain 'X' and resid 189 through 199 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) Processing helix chain 'X' and resid 214 through 244 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 60 through 62 No H-bonds generated for 'chain 'Z' and resid 60 through 62' Processing helix chain 'Z' and resid 65 through 71 removed outlier: 3.536A pdb=" N VAL Z 69 " --> pdb=" O PHE Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 102 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 118 through 125 Processing helix chain '7' and resid 136 through 141 Processing helix chain '7' and resid 143 through 154 removed outlier: 4.680A pdb=" N LYS 7 148 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS 7 154 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 55 No H-bonds generated for 'chain 'U' and resid 52 through 55' Processing helix chain 'U' and resid 64 through 82 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 10 through 28 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) removed outlier: 3.715A pdb=" N SER J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 714 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: 1.96 Time building geometry restraints manager: 4.19 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: 99.13 - 106.64: 237 106.64 - 114.14: 5398 114.14 - 121.65: 5195 121.65 - 129.16: 1752 129.16 - 136.67: 37 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: 1461 2.75 - 3.29: 9012 3.29 - 3.82: 15353 3.82 - 4.36: 18111 4.36 - 4.90: 28132 Nonbonded interactions: 72069 Sorted by model distance: nonbonded pdb=" OH TYR X 32 " pdb=" O PHE X 109 " model vdw 2.208 2.440 nonbonded pdb=" O ALA L 12 " pdb=" OG1 THR L 16 " model vdw 2.249 2.440 nonbonded pdb=" O LEU S 57 " pdb=" OG1 THR S 61 " model vdw 2.259 2.440 nonbonded pdb=" O ASN Z 53 " pdb=" OG SER Z 56 " model vdw 2.272 2.440 nonbonded pdb=" O VAL X 116 " pdb=" OG SER X 120 " model vdw 2.275 2.440 ... (remaining 72064 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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. 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: 0.330 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: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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= 0.454 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 8 poor density : 358 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 364 average time/residue: 0.1752 time to fit residues: 90.0721 Evaluate side-chains 264 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0802 time to fit residues: 2.0130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 2 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9314 Z= 0.233 Angle : 0.743 7.479 12619 Z= 0.372 Chirality : 0.044 0.154 1556 Planarity : 0.005 0.054 1533 Dihedral : 6.387 28.264 1275 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.20), residues: 1191 helix: -3.38 (0.13), residues: 786 sheet: None (None), residues: 0 loop : -2.43 (0.32), residues: 405 *********************** 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 334 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 329 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 332 average time/residue: 0.1753 time to fit residues: 83.1836 Evaluate side-chains 266 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 263 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0800 time to fit residues: 1.8542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9314 Z= 0.219 Angle : 0.714 7.823 12619 Z= 0.352 Chirality : 0.044 0.207 1556 Planarity : 0.004 0.036 1533 Dihedral : 5.934 26.865 1275 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.22), residues: 1191 helix: -2.77 (0.15), residues: 799 sheet: None (None), residues: 0 loop : -2.27 (0.33), residues: 392 *********************** 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 324 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 321 time to evaluate : 1.134 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 323 average time/residue: 0.1766 time to fit residues: 81.4967 Evaluate side-chains 265 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0818 time to fit residues: 1.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9314 Z= 0.181 Angle : 0.682 8.847 12619 Z= 0.329 Chirality : 0.042 0.141 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.496 25.655 1275 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.23), residues: 1191 helix: -2.30 (0.16), residues: 798 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 393 *********************** 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 338 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.116 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 338 average time/residue: 0.1730 time to fit residues: 84.1541 Evaluate side-chains 279 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0782 time to fit residues: 1.3921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9314 Z= 0.272 Angle : 0.732 8.153 12619 Z= 0.358 Chirality : 0.045 0.177 1556 Planarity : 0.004 0.037 1533 Dihedral : 5.652 25.607 1275 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 1191 helix: -2.06 (0.17), residues: 788 sheet: None (None), residues: 0 loop : -2.08 (0.33), residues: 403 *********************** 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 319 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1691 time to fit residues: 77.8951 Evaluate side-chains 265 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9314 Z= 0.212 Angle : 0.706 8.810 12619 Z= 0.339 Chirality : 0.043 0.147 1556 Planarity : 0.004 0.036 1533 Dihedral : 5.494 25.336 1275 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 1191 helix: -1.87 (0.17), residues: 795 sheet: None (None), residues: 0 loop : -1.96 (0.34), residues: 396 *********************** 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 323 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1801 time to fit residues: 82.5312 Evaluate side-chains 258 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9314 Z= 0.196 Angle : 0.718 8.945 12619 Z= 0.339 Chirality : 0.043 0.162 1556 Planarity : 0.004 0.036 1533 Dihedral : 5.375 24.718 1275 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.24), residues: 1191 helix: -1.64 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 400 *********************** 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 321 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1784 time to fit residues: 81.8192 Evaluate side-chains 269 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 0.0060 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4714 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= 0.164 Angle : 0.727 10.661 12619 Z= 0.333 Chirality : 0.042 0.143 1556 Planarity : 0.003 0.035 1533 Dihedral : 5.178 22.907 1275 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.25), residues: 1191 helix: -1.45 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 406 *********************** 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 330 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1712 time to fit residues: 81.2394 Evaluate side-chains 266 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9314 Z= 0.184 Angle : 0.739 10.198 12619 Z= 0.340 Chirality : 0.043 0.164 1556 Planarity : 0.004 0.050 1533 Dihedral : 5.179 23.482 1275 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.25), residues: 1191 helix: -1.48 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 385 *********************** 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 326 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1790 time to fit residues: 83.9872 Evaluate side-chains 267 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.0060 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 2 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5112 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= 0.169 Angle : 0.753 10.320 12619 Z= 0.340 Chirality : 0.042 0.174 1556 Planarity : 0.003 0.035 1533 Dihedral : 5.054 21.665 1275 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.25), residues: 1191 helix: -1.38 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 386 ********************** 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 331 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1713 time to fit residues: 81.9579 Evaluate side-chains 269 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 92 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 16 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 169 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 = 0.3970 r_free = 0.3970 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113346 restraints weight = 28082.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.115380 restraints weight = 18813.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116961 restraints weight = 13889.110| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5261 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= 0.167 Angle : 0.759 10.310 12619 Z= 0.340 Chirality : 0.042 0.164 1556 Planarity : 0.003 0.031 1533 Dihedral : 4.976 21.928 1275 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.25), residues: 1191 helix: -1.24 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 399 =============================================================================== Job complete usr+sys time: 2070.47 seconds wall clock time: 38 minutes 5.14 seconds (2285.14 seconds total)