Starting phenix.real_space_refine on Thu Feb 13 12:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtd_21894/02_2025/6wtd_21894.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtd_21894/02_2025/6wtd_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_21894/02_2025/6wtd_21894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtd_21894/02_2025/6wtd_21894.map" model { file = "/net/cci-nas-00/data/ceres_data/6wtd_21894/02_2025/6wtd_21894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtd_21894/02_2025/6wtd_21894.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.81, per 1000 atoms: 0.64 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 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... 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: 0.99 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: 2.20 Time building geometry restraints manager: 2.87 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: 0.420 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.130 Find NCS groups from input model: 0.330 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- 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= 0.459 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 14 HIS 0.007 0.002 HIS X 114 PHE 0.032 0.003 PHE M 70 TYR 0.016 0.002 TYR 8 39 ARG 0.005 0.001 ARG X 57 *********************** 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 : 0.993 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: 0.4704 (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: 0.7438 (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: 0.7899 (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: 0.9002 (ppp) REVERT: 8 37 ARG cc_start: 0.9047 (mtp180) cc_final: 0.8812 (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: 0.1826 time to fit residues: 94.8074 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 : 1.052 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.123137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107102 restraints weight = 27468.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109307 restraints weight = 17732.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110938 restraints weight = 12723.486| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2846 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= 0.220 Angle : 0.754 8.720 12619 Z= 0.375 Chirality : 0.044 0.155 1556 Planarity : 0.005 0.050 1533 Dihedral : 6.235 29.350 1275 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.32 % Allowed : 7.57 % Favored : 92.11 % 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: -4.90 (0.20), residues: 1191 helix: -3.36 (0.13), residues: 820 sheet: None (None), residues: 0 loop : -2.44 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 14 HIS 0.005 0.001 HIS X 137 PHE 0.031 0.002 PHE J 17 TYR 0.014 0.002 TYR U 51 ARG 0.002 0.000 ARG Q 39 *********************** 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 351 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.8036 (tp) cc_final: 0.7793 (tp) REVERT: K 43 ILE cc_start: 0.9042 (tp) cc_final: 0.8732 (tp) REVERT: L 39 ARG cc_start: 0.4855 (tmt170) cc_final: 0.4644 (tmt170) REVERT: N 3 LEU cc_start: 0.5881 (pt) cc_final: 0.5654 (pt) REVERT: N 9 TYR cc_start: 0.7552 (m-80) cc_final: 0.7316 (m-10) REVERT: N 19 LEU cc_start: 0.7933 (pt) cc_final: 0.7528 (pp) REVERT: O 50 MET cc_start: 0.6954 (ptt) cc_final: 0.4879 (ttp) REVERT: P 48 PHE cc_start: 0.7866 (t80) cc_final: 0.7603 (t80) REVERT: R 3 LEU cc_start: 0.8567 (tp) cc_final: 0.8291 (tp) REVERT: R 10 ILE cc_start: 0.9191 (pt) cc_final: 0.8988 (pt) REVERT: T 16 THR cc_start: 0.9177 (p) cc_final: 0.8615 (t) REVERT: 8 34 MET cc_start: 0.9065 (ppp) cc_final: 0.8674 (ppp) REVERT: X 58 TRP cc_start: 0.5203 (m-90) cc_final: 0.4556 (t-100) REVERT: X 63 GLU cc_start: 0.8762 (tt0) cc_final: 0.8557 (tt0) REVERT: X 69 ILE cc_start: 0.8590 (mp) cc_final: 0.8295 (mp) REVERT: X 85 TYR cc_start: 0.8344 (m-80) cc_final: 0.8042 (m-80) REVERT: X 169 ARG cc_start: 0.7548 (ttm170) cc_final: 0.7346 (ttm110) REVERT: X 199 MET cc_start: 0.5049 (tmm) cc_final: 0.3665 (tpp) REVERT: 7 131 ASP cc_start: 0.7249 (m-30) cc_final: 0.6797 (m-30) REVERT: 7 150 GLU cc_start: 0.8804 (tp30) cc_final: 0.8148 (tp30) REVERT: 7 154 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8250 (mtpp) REVERT: 7 169 ASN cc_start: 0.8359 (m-40) cc_final: 0.8099 (m-40) REVERT: U 48 LEU cc_start: 0.7846 (mp) cc_final: 0.7325 (mp) REVERT: J 9 ILE cc_start: 0.6239 (pt) cc_final: 0.5727 (mt) outliers start: 3 outliers final: 2 residues processed: 350 average time/residue: 0.1820 time to fit residues: 91.0709 Evaluate side-chains 271 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 0.0170 chunk 75 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 40 ASN Z 93 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 = 0.3936 r_free = 0.3936 target = 0.125799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110200 restraints weight = 27073.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112392 restraints weight = 17518.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.113879 restraints weight = 12648.197| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3581 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= 0.185 Angle : 0.700 8.977 12619 Z= 0.342 Chirality : 0.043 0.232 1556 Planarity : 0.004 0.035 1533 Dihedral : 5.613 27.252 1275 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.11 % Allowed : 6.49 % Favored : 93.41 % 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: -4.11 (0.22), residues: 1191 helix: -2.63 (0.15), residues: 844 sheet: None (None), residues: 0 loop : -2.41 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 67 HIS 0.008 0.001 HIS U 68 PHE 0.019 0.001 PHE N 64 TYR 0.016 0.001 TYR U 31 ARG 0.005 0.000 ARG Q 39 *********************** 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 354 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 1.010 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: 0.9012 (tp) cc_final: 0.8695 (tp) REVERT: L 16 THR cc_start: 0.8159 (t) cc_final: 0.7864 (m) REVERT: L 39 ARG cc_start: 0.5002 (tmt170) cc_final: 0.4734 (tmt170) REVERT: M 44 LYS cc_start: 0.7808 (tmmt) cc_final: 0.7357 (tmtt) REVERT: N 9 TYR cc_start: 0.7387 (m-80) cc_final: 0.7160 (m-10) REVERT: N 59 GLU cc_start: 0.7301 (tt0) cc_final: 0.6404 (pt0) REVERT: O 50 MET cc_start: 0.6648 (ptt) cc_final: 0.5122 (ttp) REVERT: P 67 MET cc_start: 0.7872 (mmm) cc_final: 0.7612 (tpp) REVERT: Q 63 LEU cc_start: 0.8089 (mm) cc_final: 0.7124 (pp) REVERT: S 44 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8505 (tptt) REVERT: T 16 THR cc_start: 0.9103 (p) cc_final: 0.8529 (t) REVERT: T 67 MET cc_start: 0.7456 (ppp) cc_final: 0.7227 (ppp) REVERT: 8 34 MET cc_start: 0.9096 (ppp) cc_final: 0.8590 (ppp) REVERT: X 38 LEU cc_start: 0.8650 (tt) cc_final: 0.8288 (tp) REVERT: X 63 GLU cc_start: 0.8687 (tt0) cc_final: 0.8216 (tm-30) REVERT: X 85 TYR cc_start: 0.8335 (m-80) cc_final: 0.8070 (m-80) REVERT: X 199 MET cc_start: 0.5099 (tmm) cc_final: 0.4874 (tmm) REVERT: X 216 ILE cc_start: 0.9361 (mp) cc_final: 0.8873 (mp) REVERT: Z 85 MET cc_start: 0.8051 (ptp) cc_final: 0.7850 (ptp) REVERT: Z 93 ASN cc_start: 0.8451 (m-40) cc_final: 0.8111 (t0) REVERT: 7 150 GLU cc_start: 0.8758 (tp30) cc_final: 0.8158 (tp30) REVERT: 7 154 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8235 (mtpp) REVERT: 7 169 ASN cc_start: 0.8136 (m-40) cc_final: 0.7873 (m-40) REVERT: 7 170 LEU cc_start: 0.8770 (mp) cc_final: 0.7960 (mp) REVERT: U 48 LEU cc_start: 0.7831 (mp) cc_final: 0.7554 (mp) REVERT: J 2 LEU cc_start: 0.7729 (mt) cc_final: 0.7525 (mt) REVERT: J 9 ILE cc_start: 0.6253 (pt) cc_final: 0.5717 (mt) REVERT: J 10 LEU cc_start: 0.8087 (mp) cc_final: 0.7781 (mt) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.1849 time to fit residues: 92.6517 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 : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.126281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.110337 restraints weight = 27124.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112509 restraints weight = 17690.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114049 restraints weight = 12852.274| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3971 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= 0.190 Angle : 0.696 7.809 12619 Z= 0.336 Chirality : 0.043 0.161 1556 Planarity : 0.004 0.034 1533 Dihedral : 5.372 25.963 1275 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.23), residues: 1191 helix: -2.18 (0.16), residues: 839 sheet: None (None), residues: 0 loop : -2.34 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 126 HIS 0.002 0.001 HIS X 114 PHE 0.025 0.001 PHE Z 62 TYR 0.013 0.001 TYR S 9 ARG 0.003 0.000 ARG Z 84 *********************** 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 350 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.074 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: K 43 ILE cc_start: 0.9055 (tp) cc_final: 0.8715 (tp) REVERT: K 73 LEU cc_start: 0.3830 (mp) cc_final: 0.2734 (tt) REVERT: L 16 THR cc_start: 0.8273 (t) cc_final: 0.7964 (m) REVERT: L 39 ARG cc_start: 0.5224 (tmt170) cc_final: 0.4923 (tmt170) REVERT: M 44 LYS cc_start: 0.7813 (tmmt) cc_final: 0.7378 (tmtt) REVERT: N 9 TYR cc_start: 0.7392 (m-80) cc_final: 0.7164 (m-10) REVERT: N 59 GLU cc_start: 0.7445 (tt0) cc_final: 0.6614 (pt0) REVERT: O 50 MET cc_start: 0.6628 (ptt) cc_final: 0.5055 (ttp) REVERT: P 39 ARG cc_start: 0.7052 (tpm170) cc_final: 0.6764 (tpm170) REVERT: P 67 MET cc_start: 0.7770 (mmm) cc_final: 0.7470 (tpp) REVERT: Q 63 LEU cc_start: 0.8113 (mm) cc_final: 0.7144 (pp) REVERT: R 10 ILE cc_start: 0.9212 (pt) cc_final: 0.9011 (pt) REVERT: R 14 ILE cc_start: 0.9194 (tp) cc_final: 0.8933 (tp) REVERT: S 44 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8496 (tptt) REVERT: T 16 THR cc_start: 0.9055 (p) cc_final: 0.8532 (t) REVERT: T 45 ASP cc_start: 0.8311 (p0) cc_final: 0.8031 (p0) REVERT: 8 34 MET cc_start: 0.9144 (ppp) cc_final: 0.8588 (ppp) REVERT: X 38 LEU cc_start: 0.8708 (tt) cc_final: 0.8350 (tp) REVERT: X 63 GLU cc_start: 0.8641 (tt0) cc_final: 0.8181 (tm-30) REVERT: X 85 TYR cc_start: 0.8321 (m-80) cc_final: 0.8107 (m-80) REVERT: X 216 ILE cc_start: 0.9389 (mp) cc_final: 0.8999 (mp) REVERT: 7 150 GLU cc_start: 0.8692 (tp30) cc_final: 0.8088 (tp30) REVERT: 7 154 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8064 (mtpp) REVERT: 7 170 LEU cc_start: 0.8730 (mp) cc_final: 0.8222 (mp) REVERT: J 9 ILE cc_start: 0.6552 (pt) cc_final: 0.5978 (mt) REVERT: J 10 LEU cc_start: 0.8002 (mp) cc_final: 0.7756 (mp) REVERT: J 23 VAL cc_start: 0.9532 (t) cc_final: 0.9321 (t) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1835 time to fit residues: 91.9361 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 : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 35 ASN X 114 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.127872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.112017 restraints weight = 27602.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114189 restraints weight = 18134.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.115565 restraints weight = 13197.016| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9314 Z= 0.174 Angle : 0.687 8.924 12619 Z= 0.325 Chirality : 0.042 0.171 1556 Planarity : 0.004 0.035 1533 Dihedral : 5.148 23.647 1275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.08 (0.23), residues: 1191 helix: -1.79 (0.17), residues: 826 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 158 HIS 0.001 0.001 HIS U 68 PHE 0.021 0.001 PHE S 70 TYR 0.011 0.001 TYR T 9 ARG 0.006 0.000 ARG Z 84 *********************** 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 352 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 52 ILE cc_start: 0.8438 (mm) cc_final: 0.8184 (mm) REVERT: K 73 LEU cc_start: 0.4031 (mp) cc_final: 0.3227 (tt) REVERT: L 16 THR cc_start: 0.8270 (t) cc_final: 0.7956 (m) REVERT: L 39 ARG cc_start: 0.5232 (tmt170) cc_final: 0.4900 (tmt170) REVERT: M 44 LYS cc_start: 0.7784 (tmmt) cc_final: 0.7344 (tmtt) REVERT: N 9 TYR cc_start: 0.7317 (m-80) cc_final: 0.7111 (m-10) REVERT: N 19 LEU cc_start: 0.7903 (pt) cc_final: 0.7545 (pp) REVERT: N 52 ILE cc_start: 0.7924 (mt) cc_final: 0.7659 (mm) REVERT: N 59 GLU cc_start: 0.7569 (tt0) cc_final: 0.6819 (pt0) REVERT: P 39 ARG cc_start: 0.7012 (tpm170) cc_final: 0.6785 (tpm170) REVERT: P 40 ASN cc_start: 0.7715 (t0) cc_final: 0.7499 (t0) REVERT: P 67 MET cc_start: 0.7759 (mmm) cc_final: 0.7311 (tpp) REVERT: Q 63 LEU cc_start: 0.7898 (mm) cc_final: 0.7035 (pp) REVERT: R 14 ILE cc_start: 0.9159 (tp) cc_final: 0.8924 (tp) REVERT: R 59 GLU cc_start: 0.5853 (tt0) cc_final: 0.5592 (tt0) REVERT: T 16 THR cc_start: 0.8904 (p) cc_final: 0.8381 (t) REVERT: T 45 ASP cc_start: 0.8275 (p0) cc_final: 0.7986 (p0) REVERT: T 67 MET cc_start: 0.7638 (ppp) cc_final: 0.7415 (ppp) REVERT: 8 34 MET cc_start: 0.9085 (ppp) cc_final: 0.8745 (ppp) REVERT: X 38 LEU cc_start: 0.8732 (tt) cc_final: 0.8370 (tp) REVERT: X 85 TYR cc_start: 0.8387 (m-80) cc_final: 0.8043 (m-80) REVERT: X 236 ILE cc_start: 0.9370 (mm) cc_final: 0.9080 (mt) REVERT: 7 150 GLU cc_start: 0.8538 (tp30) cc_final: 0.8073 (tp30) REVERT: 7 154 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8422 (ttmm) REVERT: 7 169 ASN cc_start: 0.8255 (m-40) cc_final: 0.7964 (m110) REVERT: J 9 ILE cc_start: 0.6613 (pt) cc_final: 0.5944 (mt) REVERT: J 10 LEU cc_start: 0.8005 (mp) cc_final: 0.7715 (mt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1838 time to fit residues: 92.6614 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 : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.125459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109816 restraints weight = 27562.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.111895 restraints weight = 18232.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113250 restraints weight = 13445.296| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4449 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= 0.216 Angle : 0.701 8.873 12619 Z= 0.340 Chirality : 0.043 0.143 1556 Planarity : 0.004 0.033 1533 Dihedral : 5.161 24.767 1275 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.66 (0.24), residues: 1191 helix: -1.53 (0.17), residues: 835 sheet: None (None), residues: 0 loop : -1.91 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 126 HIS 0.002 0.001 HIS X 137 PHE 0.023 0.002 PHE Z 62 TYR 0.014 0.001 TYR T 9 ARG 0.007 0.001 ARG Z 84 *********************** 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 341 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 52 ILE cc_start: 0.8557 (mm) cc_final: 0.8278 (mm) REVERT: L 16 THR cc_start: 0.8388 (t) cc_final: 0.8071 (m) REVERT: L 39 ARG cc_start: 0.5484 (tmt170) cc_final: 0.5010 (tmt170) REVERT: M 44 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7436 (tmtt) REVERT: N 9 TYR cc_start: 0.7289 (m-80) cc_final: 0.7040 (m-10) REVERT: N 40 ASN cc_start: 0.8661 (t0) cc_final: 0.8325 (t0) REVERT: N 59 GLU cc_start: 0.7379 (tt0) cc_final: 0.6673 (pt0) REVERT: P 67 MET cc_start: 0.7734 (mmm) cc_final: 0.7466 (tpp) REVERT: Q 61 THR cc_start: 0.8345 (t) cc_final: 0.7975 (m) REVERT: Q 63 LEU cc_start: 0.7889 (mm) cc_final: 0.7039 (pp) REVERT: T 16 THR cc_start: 0.8906 (p) cc_final: 0.8390 (t) REVERT: T 45 ASP cc_start: 0.8322 (p0) cc_final: 0.8075 (p0) REVERT: 8 34 MET cc_start: 0.9100 (ppp) cc_final: 0.8745 (ppp) REVERT: X 38 LEU cc_start: 0.8724 (tt) cc_final: 0.8380 (tp) REVERT: X 63 GLU cc_start: 0.8651 (tt0) cc_final: 0.8443 (tm-30) REVERT: 7 150 GLU cc_start: 0.8545 (tp30) cc_final: 0.8081 (tp30) REVERT: 7 154 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8265 (mtpp) REVERT: 7 164 LYS cc_start: 0.8760 (mmpt) cc_final: 0.8515 (mmmt) REVERT: 7 170 LEU cc_start: 0.8818 (mp) cc_final: 0.7246 (mp) REVERT: U 79 SER cc_start: 0.8158 (m) cc_final: 0.7737 (p) REVERT: J 9 ILE cc_start: 0.6792 (pt) cc_final: 0.6107 (mt) REVERT: J 10 LEU cc_start: 0.8109 (mp) cc_final: 0.7844 (mt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1739 time to fit residues: 86.0950 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 : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3962 r_free = 0.3962 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.111017 restraints weight = 28286.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.113145 restraints weight = 18767.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114663 restraints weight = 13744.003| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4668 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= 0.195 Angle : 0.717 9.441 12619 Z= 0.341 Chirality : 0.043 0.218 1556 Planarity : 0.003 0.033 1533 Dihedral : 5.059 23.897 1275 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.24), residues: 1191 helix: -1.39 (0.18), residues: 823 sheet: None (None), residues: 0 loop : -1.92 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 126 HIS 0.001 0.000 HIS X 185 PHE 0.040 0.002 PHE S 70 TYR 0.016 0.001 TYR X 232 ARG 0.006 0.000 ARG Z 84 *********************** 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 345 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7635 (tp) cc_final: 0.7237 (tp) REVERT: L 16 THR cc_start: 0.8377 (t) cc_final: 0.8081 (m) REVERT: L 39 ARG cc_start: 0.5273 (tmt170) cc_final: 0.5053 (tmt170) REVERT: M 44 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7481 (tmtt) REVERT: N 9 TYR cc_start: 0.7268 (m-80) cc_final: 0.7017 (m-10) REVERT: N 19 LEU cc_start: 0.7918 (pt) cc_final: 0.7694 (pp) REVERT: N 40 ASN cc_start: 0.8613 (t0) cc_final: 0.8265 (t0) REVERT: N 52 ILE cc_start: 0.7842 (mt) cc_final: 0.7581 (mm) REVERT: O 50 MET cc_start: 0.6597 (ptt) cc_final: 0.5674 (ptm) REVERT: P 39 ARG cc_start: 0.6768 (tpm170) cc_final: 0.6509 (tpm170) REVERT: P 40 ASN cc_start: 0.7755 (t0) cc_final: 0.7547 (t0) REVERT: P 67 MET cc_start: 0.7656 (mmm) cc_final: 0.7199 (tpp) REVERT: Q 61 THR cc_start: 0.8344 (t) cc_final: 0.8028 (m) REVERT: Q 63 LEU cc_start: 0.7953 (mm) cc_final: 0.7190 (pp) REVERT: R 59 GLU cc_start: 0.5938 (tt0) cc_final: 0.5591 (tt0) REVERT: S 67 MET cc_start: 0.8302 (tpt) cc_final: 0.8022 (tpt) REVERT: T 16 THR cc_start: 0.8785 (p) cc_final: 0.8130 (t) REVERT: T 45 ASP cc_start: 0.8323 (p0) cc_final: 0.8122 (p0) REVERT: 8 34 MET cc_start: 0.9112 (ppp) cc_final: 0.8790 (ppp) REVERT: X 38 LEU cc_start: 0.8729 (tt) cc_final: 0.8380 (tp) REVERT: X 63 GLU cc_start: 0.8707 (tt0) cc_final: 0.8458 (tm-30) REVERT: 7 150 GLU cc_start: 0.8615 (tp30) cc_final: 0.8150 (tp30) REVERT: 7 152 MET cc_start: 0.7991 (ptp) cc_final: 0.7349 (ptp) REVERT: 7 154 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8322 (mtpp) REVERT: 7 164 LYS cc_start: 0.8887 (mmpt) cc_final: 0.8651 (mmmt) REVERT: 7 170 LEU cc_start: 0.8768 (mp) cc_final: 0.7226 (mp) REVERT: 7 171 ASN cc_start: 0.8400 (p0) cc_final: 0.8087 (p0) REVERT: U 79 SER cc_start: 0.8141 (m) cc_final: 0.7741 (p) REVERT: J 9 ILE cc_start: 0.6666 (pt) cc_final: 0.6218 (mt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1831 time to fit residues: 91.3530 Evaluate side-chains 287 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 2 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112833 restraints weight = 28096.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114988 restraints weight = 18509.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116538 restraints weight = 13430.157| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4927 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= 0.177 Angle : 0.731 10.663 12619 Z= 0.339 Chirality : 0.043 0.176 1556 Planarity : 0.004 0.041 1533 Dihedral : 4.932 22.660 1275 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.11 % Allowed : 1.30 % 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 (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: -2.23 (0.25), residues: 1191 helix: -1.16 (0.18), residues: 825 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 126 HIS 0.004 0.001 HIS U 29 PHE 0.026 0.001 PHE Z 62 TYR 0.013 0.001 TYR T 9 ARG 0.006 0.000 ARG Z 84 *********************** 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 351 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7612 (tp) cc_final: 0.7121 (tp) REVERT: K 52 ILE cc_start: 0.8367 (mm) cc_final: 0.8108 (mm) REVERT: L 16 THR cc_start: 0.8268 (t) cc_final: 0.8015 (m) REVERT: M 26 ILE cc_start: 0.8442 (tt) cc_final: 0.8229 (tt) REVERT: M 44 LYS cc_start: 0.7917 (tmmt) cc_final: 0.7513 (tmtt) REVERT: N 9 TYR cc_start: 0.7216 (m-80) cc_final: 0.6952 (m-10) REVERT: N 19 LEU cc_start: 0.7919 (pt) cc_final: 0.7717 (pp) REVERT: N 40 ASN cc_start: 0.8599 (t0) cc_final: 0.8265 (t0) REVERT: O 50 MET cc_start: 0.6057 (ptt) cc_final: 0.4215 (ttp) REVERT: P 24 ILE cc_start: 0.6848 (mm) cc_final: 0.6368 (mm) REVERT: P 40 ASN cc_start: 0.7801 (t0) cc_final: 0.7591 (t0) REVERT: P 67 MET cc_start: 0.7703 (mmm) cc_final: 0.7080 (tpp) REVERT: Q 61 THR cc_start: 0.8195 (t) cc_final: 0.7937 (m) REVERT: Q 63 LEU cc_start: 0.7865 (mm) cc_final: 0.7199 (pp) REVERT: R 59 GLU cc_start: 0.6030 (tt0) cc_final: 0.5795 (tt0) REVERT: T 16 THR cc_start: 0.8850 (p) cc_final: 0.8256 (t) REVERT: T 45 ASP cc_start: 0.8321 (p0) cc_final: 0.8112 (p0) REVERT: 8 34 MET cc_start: 0.9082 (ppp) cc_final: 0.8788 (ppp) REVERT: 8 39 TYR cc_start: 0.8516 (m-80) cc_final: 0.7954 (m-80) REVERT: X 38 LEU cc_start: 0.8678 (tt) cc_final: 0.8360 (tp) REVERT: X 63 GLU cc_start: 0.8730 (tt0) cc_final: 0.8179 (tm-30) REVERT: X 105 ILE cc_start: 0.8641 (mm) cc_final: 0.8420 (tt) REVERT: Z 90 ASP cc_start: 0.8041 (p0) cc_final: 0.7524 (m-30) REVERT: 7 154 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8434 (ttpt) REVERT: 7 170 LEU cc_start: 0.8772 (mp) cc_final: 0.8320 (mt) REVERT: U 79 SER cc_start: 0.8129 (m) cc_final: 0.7675 (p) REVERT: J 9 ILE cc_start: 0.6567 (pt) cc_final: 0.6233 (mt) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.1707 time to fit residues: 87.3095 Evaluate side-chains 295 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 114 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.124320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108856 restraints weight = 28356.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110894 restraints weight = 19014.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112276 restraints weight = 13972.054| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9314 Z= 0.284 Angle : 0.785 9.595 12619 Z= 0.379 Chirality : 0.046 0.163 1556 Planarity : 0.004 0.034 1533 Dihedral : 5.186 24.094 1275 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.25), residues: 1191 helix: -1.31 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 126 HIS 0.003 0.001 HIS X 137 PHE 0.019 0.002 PHE U 76 TYR 0.015 0.001 TYR X 232 ARG 0.011 0.001 ARG Z 84 *********************** 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 334 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7856 (tp) cc_final: 0.7559 (tp) REVERT: K 52 ILE cc_start: 0.8438 (mm) cc_final: 0.8168 (mm) REVERT: M 44 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7671 (tmmt) REVERT: N 9 TYR cc_start: 0.7309 (m-80) cc_final: 0.7047 (m-10) REVERT: N 40 ASN cc_start: 0.8697 (t0) cc_final: 0.8317 (t0) REVERT: O 50 MET cc_start: 0.6358 (ptt) cc_final: 0.5345 (ptm) REVERT: P 67 MET cc_start: 0.7610 (mmm) cc_final: 0.7331 (tpp) REVERT: Q 61 THR cc_start: 0.8220 (t) cc_final: 0.7910 (m) REVERT: Q 63 LEU cc_start: 0.8044 (mm) cc_final: 0.7269 (pp) REVERT: T 16 THR cc_start: 0.8856 (p) cc_final: 0.8417 (t) REVERT: 8 34 MET cc_start: 0.9160 (ppp) cc_final: 0.8865 (ppp) REVERT: X 38 LEU cc_start: 0.8767 (tt) cc_final: 0.8393 (tp) REVERT: X 63 GLU cc_start: 0.8729 (tt0) cc_final: 0.8447 (tm-30) REVERT: 7 150 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7891 (tm-30) REVERT: 7 152 MET cc_start: 0.7992 (ptp) cc_final: 0.7420 (ptp) REVERT: 7 157 LYS cc_start: 0.8803 (tmmt) cc_final: 0.8344 (ttpt) REVERT: 7 170 LEU cc_start: 0.8745 (mp) cc_final: 0.7461 (mp) REVERT: U 79 SER cc_start: 0.8126 (m) cc_final: 0.7833 (p) REVERT: J 9 ILE cc_start: 0.6608 (pt) cc_final: 0.6260 (mt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1676 time to fit residues: 82.0408 Evaluate side-chains 276 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN X 114 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.128601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112562 restraints weight = 28240.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114727 restraints weight = 18601.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116293 restraints weight = 13584.185| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5086 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= 0.183 Angle : 0.773 11.058 12619 Z= 0.355 Chirality : 0.043 0.154 1556 Planarity : 0.004 0.038 1533 Dihedral : 4.990 23.409 1275 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.25), residues: 1191 helix: -0.95 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 14 HIS 0.003 0.001 HIS X 185 PHE 0.022 0.001 PHE K 30 TYR 0.016 0.001 TYR T 9 ARG 0.008 0.001 ARG Z 84 ********************** 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 337 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7583 (tp) cc_final: 0.7265 (tp) REVERT: K 52 ILE cc_start: 0.8206 (mm) cc_final: 0.7987 (mm) REVERT: M 44 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7451 (tmtt) REVERT: N 9 TYR cc_start: 0.7290 (m-80) cc_final: 0.7000 (m-10) REVERT: N 40 ASN cc_start: 0.8643 (t0) cc_final: 0.8256 (t0) REVERT: P 67 MET cc_start: 0.7539 (mmm) cc_final: 0.7166 (tpp) REVERT: Q 61 THR cc_start: 0.8161 (t) cc_final: 0.7890 (m) REVERT: Q 63 LEU cc_start: 0.7849 (mm) cc_final: 0.7220 (pp) REVERT: R 47 VAL cc_start: 0.8781 (m) cc_final: 0.8360 (p) REVERT: T 16 THR cc_start: 0.8820 (p) cc_final: 0.8338 (t) REVERT: 8 34 MET cc_start: 0.9107 (ppp) cc_final: 0.8818 (ppp) REVERT: 8 39 TYR cc_start: 0.8649 (m-80) cc_final: 0.8014 (m-80) REVERT: X 38 LEU cc_start: 0.8731 (tt) cc_final: 0.8383 (tp) REVERT: X 63 GLU cc_start: 0.8733 (tt0) cc_final: 0.8132 (tm-30) REVERT: X 105 ILE cc_start: 0.8654 (mm) cc_final: 0.8378 (tt) REVERT: Z 90 ASP cc_start: 0.7967 (p0) cc_final: 0.7438 (m-30) REVERT: 7 150 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7805 (tm-30) REVERT: 7 170 LEU cc_start: 0.8744 (mp) cc_final: 0.8183 (mt) REVERT: U 76 PHE cc_start: 0.8623 (t80) cc_final: 0.8323 (t80) REVERT: U 79 SER cc_start: 0.8019 (m) cc_final: 0.7750 (p) REVERT: J 9 ILE cc_start: 0.6566 (pt) cc_final: 0.6244 (mt) REVERT: J 23 VAL cc_start: 0.9401 (t) cc_final: 0.9195 (t) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1676 time to fit residues: 82.8986 Evaluate side-chains 295 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN X 114 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.128675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113070 restraints weight = 28110.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115168 restraints weight = 18526.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.116686 restraints weight = 13490.687| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5197 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= 0.191 Angle : 0.757 9.899 12619 Z= 0.350 Chirality : 0.043 0.151 1556 Planarity : 0.004 0.032 1533 Dihedral : 4.913 22.975 1275 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.25), residues: 1191 helix: -0.92 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 126 HIS 0.001 0.000 HIS X 185 PHE 0.014 0.001 PHE K 30 TYR 0.025 0.001 TYR X 232 ARG 0.008 0.001 ARG Z 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.24 seconds wall clock time: 51 minutes 42.42 seconds (3102.42 seconds total)