Starting phenix.real_space_refine on Thu Mar 13 14:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtd_21894/03_2025/6wtd_21894.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtd_21894/03_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_21894/03_2025/6wtd_21894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2025/6wtd_21894.map" model { file = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_2025/6wtd_21894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtd_21894/03_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-5624/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: 5.86, 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: 2.28 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: 0.95 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: 2.72 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.370 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- 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 : 1.054 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: 0.1844 time to fit residues: 94.9919 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 : 1.056 ------------------------------------------------------------------------------- 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 = 0.123138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.107104 restraints weight = 27468.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109295 restraints weight = 17733.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110940 restraints weight = 12716.721| |-----------------------------------------------------------------------------| 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 8.719 12619 Z= 0.375 Chirality : 0.044 0.155 1556 Planarity : 0.005 0.050 1533 Dihedral : 6.235 29.348 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 : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.8035 (tp) cc_final: 0.7792 (tp) REVERT: K 43 ILE cc_start: 0.9042 (tp) cc_final: 0.8732 (tp) REVERT: L 39 ARG cc_start: 0.4854 (tmt170) cc_final: 0.4645 (tmt170) REVERT: N 3 LEU cc_start: 0.5882 (pt) cc_final: 0.5655 (pt) REVERT: N 9 TYR cc_start: 0.7558 (m-80) cc_final: 0.7320 (m-10) REVERT: N 19 LEU cc_start: 0.7934 (pt) cc_final: 0.7530 (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: 0.7604 (t80) REVERT: R 3 LEU cc_start: 0.8567 (tp) cc_final: 0.8291 (tp) REVERT: R 10 ILE cc_start: 0.9193 (pt) cc_final: 0.8989 (pt) REVERT: T 16 THR cc_start: 0.9177 (p) cc_final: 0.8616 (t) REVERT: 8 34 MET cc_start: 0.9065 (ppp) cc_final: 0.8674 (ppp) REVERT: X 58 TRP cc_start: 0.5206 (m-90) cc_final: 0.4555 (t-100) REVERT: X 63 GLU cc_start: 0.8764 (tt0) cc_final: 0.8559 (tt0) REVERT: X 69 ILE cc_start: 0.8590 (mp) cc_final: 0.8296 (mp) REVERT: X 85 TYR cc_start: 0.8340 (m-80) cc_final: 0.8041 (m-80) REVERT: X 169 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7346 (ttm110) REVERT: X 199 MET cc_start: 0.5045 (tmm) cc_final: 0.3664 (tpp) REVERT: 7 131 ASP cc_start: 0.7248 (m-30) cc_final: 0.6796 (m-30) REVERT: 7 150 GLU cc_start: 0.8804 (tp30) cc_final: 0.8149 (tp30) REVERT: 7 154 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8249 (mtpp) REVERT: 7 169 ASN cc_start: 0.8359 (m-40) cc_final: 0.8098 (m-40) REVERT: U 48 LEU cc_start: 0.7846 (mp) cc_final: 0.7324 (mp) REVERT: J 9 ILE cc_start: 0.6240 (pt) cc_final: 0.5728 (mt) outliers start: 3 outliers final: 2 residues processed: 350 average time/residue: 0.1756 time to fit residues: 88.5742 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 : 1.094 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 0.0050 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 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 = 0.3951 r_free = 0.3951 target = 0.126796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111090 restraints weight = 27014.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113342 restraints weight = 17485.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114813 restraints weight = 12580.905| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9314 Z= 0.178 Angle : 0.699 9.410 12619 Z= 0.340 Chirality : 0.043 0.217 1556 Planarity : 0.004 0.035 1533 Dihedral : 5.547 26.767 1275 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.12 (0.22), residues: 1191 helix: -2.62 (0.15), residues: 842 sheet: None (None), residues: 0 loop : -2.47 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 14 HIS 0.006 0.001 HIS U 68 PHE 0.020 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 364 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 16 THR cc_start: 0.8202 (t) cc_final: 0.7839 (m) REVERT: L 39 ARG cc_start: 0.4921 (tmt170) cc_final: 0.4575 (tmt170) REVERT: M 44 LYS cc_start: 0.7841 (tmmt) cc_final: 0.7407 (tmtt) REVERT: N 9 TYR cc_start: 0.7385 (m-80) cc_final: 0.7152 (m-10) REVERT: N 59 GLU cc_start: 0.7279 (tt0) cc_final: 0.6395 (pt0) REVERT: P 67 MET cc_start: 0.7774 (mmm) cc_final: 0.7495 (tpp) REVERT: Q 63 LEU cc_start: 0.8060 (mm) cc_final: 0.7114 (pp) REVERT: S 44 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8482 (tptt) REVERT: T 16 THR cc_start: 0.9046 (p) cc_final: 0.8469 (t) REVERT: T 67 MET cc_start: 0.7235 (ppp) cc_final: 0.7029 (ppp) REVERT: 8 34 MET cc_start: 0.9088 (ppp) cc_final: 0.8590 (ppp) REVERT: X 38 LEU cc_start: 0.8641 (tt) cc_final: 0.8290 (tp) REVERT: X 63 GLU cc_start: 0.8679 (tt0) cc_final: 0.8253 (tm-30) REVERT: X 85 TYR cc_start: 0.8314 (m-80) cc_final: 0.8013 (m-80) REVERT: X 199 MET cc_start: 0.5053 (tmm) cc_final: 0.4826 (tmm) REVERT: X 216 ILE cc_start: 0.9353 (mp) cc_final: 0.8862 (mp) REVERT: X 236 ILE cc_start: 0.9387 (mm) cc_final: 0.9064 (mt) REVERT: Z 85 MET cc_start: 0.8031 (ptp) cc_final: 0.7825 (ptp) REVERT: Z 93 ASN cc_start: 0.8370 (m110) cc_final: 0.8074 (t0) REVERT: 7 150 GLU cc_start: 0.8749 (tp30) cc_final: 0.8115 (tp30) REVERT: 7 154 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8189 (mtpp) REVERT: 7 170 LEU cc_start: 0.8694 (mp) cc_final: 0.8152 (mp) REVERT: U 48 LEU cc_start: 0.7820 (mp) cc_final: 0.7551 (mp) REVERT: J 9 ILE cc_start: 0.6367 (pt) cc_final: 0.5807 (mt) REVERT: J 10 LEU cc_start: 0.8061 (mp) cc_final: 0.7761 (mt) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.1796 time to fit residues: 92.7540 Evaluate side-chains 284 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 82 optimal weight: 0.0010 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.5866 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.128331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112444 restraints weight = 26949.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114617 restraints weight = 17659.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116050 restraints weight = 12856.274| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4200 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= 0.165 Angle : 0.682 7.700 12619 Z= 0.326 Chirality : 0.042 0.155 1556 Planarity : 0.004 0.032 1533 Dihedral : 5.244 24.763 1275 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.53 (0.23), residues: 1191 helix: -2.10 (0.16), residues: 835 sheet: None (None), residues: 0 loop : -2.51 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 126 HIS 0.001 0.001 HIS X 185 PHE 0.027 0.001 PHE Z 62 TYR 0.012 0.001 TYR T 9 ARG 0.003 0.000 ARG Q 39 *********************** 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 363 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.867 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: 0.8980 (tp) cc_final: 0.8756 (tp) REVERT: K 52 ILE cc_start: 0.8533 (mm) cc_final: 0.8265 (mm) REVERT: K 73 LEU cc_start: 0.3708 (mp) cc_final: 0.2773 (tt) REVERT: L 16 THR cc_start: 0.8156 (t) cc_final: 0.7838 (m) REVERT: L 39 ARG cc_start: 0.5184 (tmt170) cc_final: 0.4872 (tmt170) REVERT: M 44 LYS cc_start: 0.7832 (tmmt) cc_final: 0.7458 (tmtt) REVERT: N 9 TYR cc_start: 0.7355 (m-80) cc_final: 0.7100 (m-10) REVERT: N 19 LEU cc_start: 0.7873 (pt) cc_final: 0.7495 (pp) REVERT: N 59 GLU cc_start: 0.7567 (tt0) cc_final: 0.6708 (pt0) REVERT: O 50 MET cc_start: 0.6622 (ptt) cc_final: 0.5683 (ptm) REVERT: P 39 ARG cc_start: 0.7085 (tpm170) cc_final: 0.6761 (tpm170) REVERT: P 67 MET cc_start: 0.7872 (mmm) cc_final: 0.7476 (tpp) REVERT: Q 63 LEU cc_start: 0.7968 (mm) cc_final: 0.7065 (pp) REVERT: R 59 GLU cc_start: 0.5805 (tt0) cc_final: 0.5572 (tt0) REVERT: S 44 LYS cc_start: 0.8756 (tmtt) cc_final: 0.8469 (tptt) REVERT: T 16 THR cc_start: 0.9030 (p) cc_final: 0.8506 (t) REVERT: T 45 ASP cc_start: 0.8287 (p0) cc_final: 0.7981 (p0) REVERT: T 67 MET cc_start: 0.7098 (ppp) cc_final: 0.6889 (ppp) REVERT: 8 34 MET cc_start: 0.9135 (ppp) cc_final: 0.8570 (ppp) REVERT: X 38 LEU cc_start: 0.8716 (tt) cc_final: 0.8359 (tp) REVERT: X 63 GLU cc_start: 0.8671 (tt0) cc_final: 0.8141 (tm-30) REVERT: X 74 LYS cc_start: 0.9294 (tptp) cc_final: 0.9039 (tptp) REVERT: X 85 TYR cc_start: 0.8363 (m-80) cc_final: 0.8119 (m-80) REVERT: X 216 ILE cc_start: 0.9387 (mp) cc_final: 0.8990 (mp) REVERT: X 236 ILE cc_start: 0.9319 (mm) cc_final: 0.9044 (mt) REVERT: 7 132 GLU cc_start: 0.8572 (tp30) cc_final: 0.8062 (pt0) REVERT: 7 150 GLU cc_start: 0.8611 (tp30) cc_final: 0.8137 (tp30) REVERT: 7 154 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8375 (ttmm) REVERT: 7 170 LEU cc_start: 0.9045 (mp) cc_final: 0.8537 (mt) REVERT: J 9 ILE cc_start: 0.6479 (pt) cc_final: 0.5918 (mt) REVERT: J 10 LEU cc_start: 0.7875 (mp) cc_final: 0.7635 (mp) REVERT: J 23 VAL cc_start: 0.9490 (t) cc_final: 0.9254 (t) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1817 time to fit residues: 93.4687 Evaluate side-chains 296 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 24 optimal weight: 0.0970 chunk 109 optimal weight: 7.9990 chunk 4 optimal weight: 0.0970 chunk 39 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 2 GLN 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 = 0.3982 r_free = 0.3982 target = 0.128702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112821 restraints weight = 27657.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114946 restraints weight = 18249.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116313 restraints weight = 13332.195| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4575 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= 0.173 Angle : 0.685 8.802 12619 Z= 0.323 Chirality : 0.043 0.161 1556 Planarity : 0.004 0.033 1533 Dihedral : 5.044 22.687 1275 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.11 % Allowed : 3.46 % Favored : 96.43 % 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: -2.95 (0.24), residues: 1191 helix: -1.67 (0.17), residues: 826 sheet: None (None), residues: 0 loop : -2.27 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 58 HIS 0.001 0.001 HIS U 68 PHE 0.018 0.001 PHE S 70 TYR 0.018 0.001 TYR J 25 ARG 0.002 0.000 ARG 7 128 *********************** 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 359 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 43 ILE cc_start: 0.9021 (tp) cc_final: 0.8762 (tp) REVERT: K 52 ILE cc_start: 0.8401 (mm) cc_final: 0.8073 (mm) REVERT: K 73 LEU cc_start: 0.4004 (mp) cc_final: 0.3204 (tt) REVERT: L 16 THR cc_start: 0.8240 (t) cc_final: 0.7855 (m) REVERT: L 39 ARG cc_start: 0.5120 (tmt170) cc_final: 0.4759 (tmt170) REVERT: M 44 LYS cc_start: 0.7846 (tmmt) cc_final: 0.7493 (tmtt) REVERT: N 9 TYR cc_start: 0.7332 (m-80) cc_final: 0.7065 (m-10) REVERT: N 40 ASN cc_start: 0.8628 (t0) cc_final: 0.8280 (t0) REVERT: N 52 ILE cc_start: 0.7817 (mt) cc_final: 0.7557 (mm) REVERT: N 59 GLU cc_start: 0.7519 (tt0) cc_final: 0.6754 (pt0) REVERT: O 34 ILE cc_start: 0.7796 (mt) cc_final: 0.7256 (mt) REVERT: P 39 ARG cc_start: 0.7187 (tpm170) cc_final: 0.6972 (tpm170) REVERT: P 67 MET cc_start: 0.7886 (mmm) cc_final: 0.7408 (tpp) REVERT: Q 61 THR cc_start: 0.8371 (t) cc_final: 0.8027 (m) REVERT: Q 63 LEU cc_start: 0.7883 (mm) cc_final: 0.7056 (pp) REVERT: R 14 ILE cc_start: 0.9076 (tp) cc_final: 0.8811 (tp) REVERT: R 59 GLU cc_start: 0.5900 (tt0) cc_final: 0.5521 (tt0) REVERT: S 44 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8565 (tptt) REVERT: T 16 THR cc_start: 0.8792 (p) cc_final: 0.8244 (t) REVERT: T 45 ASP cc_start: 0.8317 (p0) cc_final: 0.7980 (p0) REVERT: 8 34 MET cc_start: 0.9142 (ppp) cc_final: 0.8786 (ppp) REVERT: X 38 LEU cc_start: 0.8725 (tt) cc_final: 0.8391 (tp) REVERT: X 63 GLU cc_start: 0.8664 (tt0) cc_final: 0.8115 (tm-30) REVERT: X 74 LYS cc_start: 0.9272 (tptp) cc_final: 0.8948 (tppt) REVERT: X 85 TYR cc_start: 0.8341 (m-80) cc_final: 0.7995 (m-80) REVERT: Z 85 MET cc_start: 0.8266 (ptp) cc_final: 0.8051 (ptp) REVERT: 7 132 GLU cc_start: 0.8614 (tp30) cc_final: 0.8051 (pt0) REVERT: 7 150 GLU cc_start: 0.8591 (tp30) cc_final: 0.8099 (tp30) REVERT: 7 152 MET cc_start: 0.7970 (ptp) cc_final: 0.7239 (ptp) REVERT: 7 154 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8262 (mtpp) REVERT: 7 170 LEU cc_start: 0.8998 (mp) cc_final: 0.8417 (mt) REVERT: J 9 ILE cc_start: 0.6633 (pt) cc_final: 0.5970 (mt) REVERT: J 10 LEU cc_start: 0.8010 (mp) cc_final: 0.7735 (mt) outliers start: 1 outliers final: 0 residues processed: 359 average time/residue: 0.1827 time to fit residues: 94.5810 Evaluate side-chains 296 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 2 GLN P 35 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 = 0.3912 r_free = 0.3912 target = 0.124037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108245 restraints weight = 27910.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110258 restraints weight = 18667.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111645 restraints weight = 13699.775| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9314 Z= 0.269 Angle : 0.753 9.832 12619 Z= 0.367 Chirality : 0.046 0.168 1556 Planarity : 0.004 0.033 1533 Dihedral : 5.294 25.666 1275 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.61 (0.24), residues: 1191 helix: -1.49 (0.17), residues: 827 sheet: None (None), residues: 0 loop : -1.90 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 126 HIS 0.003 0.001 HIS X 137 PHE 0.024 0.002 PHE K 30 TYR 0.013 0.002 TYR T 9 ARG 0.002 0.000 ARG 8 42 *********************** 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 345 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 20 LEU cc_start: 0.7731 (tp) cc_final: 0.7168 (tp) REVERT: K 39 ARG cc_start: 0.4030 (tpm170) cc_final: 0.2999 (tpm170) REVERT: M 44 LYS cc_start: 0.7842 (tmmt) cc_final: 0.7434 (tmtt) REVERT: N 9 TYR cc_start: 0.7362 (m-80) cc_final: 0.7115 (m-10) REVERT: N 40 ASN cc_start: 0.8768 (t0) cc_final: 0.8370 (t0) REVERT: O 50 MET cc_start: 0.6710 (ptt) cc_final: 0.5664 (ptm) REVERT: Q 61 THR cc_start: 0.8168 (t) cc_final: 0.7835 (m) REVERT: Q 63 LEU cc_start: 0.8026 (mm) cc_final: 0.7129 (pp) REVERT: S 44 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8567 (tptt) REVERT: T 16 THR cc_start: 0.8915 (p) cc_final: 0.8389 (t) REVERT: T 45 ASP cc_start: 0.8344 (p0) cc_final: 0.8142 (p0) REVERT: 8 34 MET cc_start: 0.9147 (ppp) cc_final: 0.8796 (ppp) REVERT: X 38 LEU cc_start: 0.8750 (tt) cc_final: 0.8411 (tp) REVERT: X 63 GLU cc_start: 0.8703 (tt0) cc_final: 0.8232 (tm-30) REVERT: 7 132 GLU cc_start: 0.8747 (tp30) cc_final: 0.8046 (pt0) REVERT: 7 150 GLU cc_start: 0.8595 (tp30) cc_final: 0.8122 (tp30) REVERT: 7 154 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8260 (mtpp) REVERT: 7 164 LYS cc_start: 0.8818 (mmpt) cc_final: 0.8547 (mmmt) REVERT: 7 170 LEU cc_start: 0.9001 (mp) cc_final: 0.8592 (mp) REVERT: J 9 ILE cc_start: 0.6689 (pt) cc_final: 0.6113 (mt) REVERT: J 10 LEU cc_start: 0.8122 (mp) cc_final: 0.7868 (mt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1727 time to fit residues: 85.5756 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 : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6561 > 50: distance: 34 - 38: 26.411 distance: 38 - 39: 11.448 distance: 39 - 40: 20.878 distance: 39 - 42: 50.169 distance: 40 - 41: 3.260 distance: 40 - 46: 27.887 distance: 41 - 72: 25.250 distance: 42 - 43: 45.590 distance: 43 - 44: 21.923 distance: 43 - 45: 37.869 distance: 46 - 47: 22.128 distance: 47 - 48: 32.603 distance: 47 - 50: 20.795 distance: 48 - 49: 25.620 distance: 48 - 53: 48.197 distance: 49 - 80: 35.731 distance: 50 - 51: 20.440 distance: 50 - 52: 43.941 distance: 53 - 54: 26.962 distance: 54 - 55: 44.048 distance: 54 - 57: 38.646 distance: 55 - 56: 43.137 distance: 55 - 64: 24.308 distance: 56 - 86: 49.142 distance: 57 - 58: 23.074 distance: 58 - 59: 15.068 distance: 58 - 60: 15.983 distance: 59 - 61: 19.045 distance: 60 - 62: 25.070 distance: 61 - 63: 6.366 distance: 62 - 63: 10.843 distance: 64 - 65: 17.078 distance: 65 - 66: 31.253 distance: 65 - 68: 15.016 distance: 66 - 67: 34.918 distance: 66 - 72: 40.081 distance: 67 - 94: 25.514 distance: 68 - 69: 22.057 distance: 68 - 70: 19.218 distance: 69 - 71: 10.372 distance: 72 - 73: 33.806 distance: 73 - 74: 17.719 distance: 73 - 76: 26.103 distance: 74 - 75: 23.842 distance: 74 - 80: 11.808 distance: 76 - 77: 22.546 distance: 76 - 78: 27.212 distance: 77 - 79: 29.824 distance: 80 - 81: 20.544 distance: 81 - 82: 32.849 distance: 81 - 84: 23.459 distance: 82 - 83: 35.569 distance: 82 - 86: 19.341 distance: 84 - 85: 18.389 distance: 86 - 87: 33.620 distance: 87 - 88: 12.702 distance: 87 - 90: 14.622 distance: 88 - 89: 27.380 distance: 88 - 94: 20.244 distance: 90 - 91: 7.473 distance: 91 - 92: 5.791 distance: 91 - 93: 5.767 distance: 94 - 95: 13.372 distance: 95 - 96: 6.270 distance: 95 - 98: 12.312 distance: 96 - 97: 9.339 distance: 96 - 100: 15.350 distance: 97 - 123: 16.447 distance: 98 - 99: 18.882 distance: 100 - 101: 32.680 distance: 101 - 102: 23.316 distance: 101 - 104: 26.568 distance: 102 - 103: 4.023 distance: 102 - 108: 19.981 distance: 103 - 132: 31.381 distance: 104 - 105: 32.916 distance: 104 - 106: 33.595 distance: 105 - 107: 15.592 distance: 108 - 109: 31.006 distance: 109 - 110: 19.086 distance: 109 - 112: 15.765 distance: 110 - 111: 11.486 distance: 110 - 115: 9.640 distance: 111 - 140: 21.923 distance: 112 - 113: 23.714 distance: 112 - 114: 27.425