Starting phenix.real_space_refine on Sat Feb 17 23:47:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdx_10470/02_2024/6tdx_10470.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6513 2.51 5 N 1609 2.21 5 O 1838 1.98 5 H 10266 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20303 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4466 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 5, 'TRANS': 270} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "0" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 462 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Time building chain proxies: 9.52, per 1000 atoms: 0.47 Number of scatterers: 20303 At special positions: 0 Unit cell: (113.4, 73.5, 180.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 O 1838 8.00 N 1609 7.00 C 6513 6.00 H 10266 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 69.4% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'G' and resid 3 through 39 removed outlier: 3.673A pdb=" N GLN G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 4.116A pdb=" N ARG G 43 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL G 44 " --> pdb=" O VAL G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 44' Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.685A pdb=" N ALA G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 removed outlier: 4.148A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 99 Processing helix chain 'G' and resid 111 through 116 removed outlier: 3.792A pdb=" N ASP G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 116' Processing helix chain 'G' and resid 116 through 121 Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.761A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 193 removed outlier: 4.296A pdb=" N GLN G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 214 removed outlier: 3.576A pdb=" N GLY G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 278 removed outlier: 4.158A pdb=" N ILE G 248 " --> pdb=" O TYR G 244 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL G 249 " --> pdb=" O ALA G 245 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN G 270 " --> pdb=" O ASP G 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.608A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 removed outlier: 3.561A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix removed outlier: 3.789A pdb=" N HIS H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 7 removed outlier: 3.569A pdb=" N GLY I 7 " --> pdb=" O TRP I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 7' Processing helix chain 'I' and resid 9 through 25 Processing helix chain 'I' and resid 28 through 35 Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'O' and resid 33 through 45 removed outlier: 4.173A pdb=" N GLY O 38 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA O 39 " --> pdb=" O ASN O 35 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY O 45 " --> pdb=" O MET O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 67 removed outlier: 3.827A pdb=" N GLY O 52 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER O 59 " --> pdb=" O MET O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 101 removed outlier: 3.744A pdb=" N LEU O 75 " --> pdb=" O SER O 71 " (cutoff:3.500A) Proline residue: O 76 - end of helix removed outlier: 3.559A pdb=" N GLU O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE O 101 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 45 removed outlier: 3.856A pdb=" N GLY P 38 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA P 39 " --> pdb=" O ASN P 35 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY P 45 " --> pdb=" O MET P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 67 removed outlier: 3.834A pdb=" N ILE P 51 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 100 removed outlier: 3.600A pdb=" N LEU P 75 " --> pdb=" O SER P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.941A pdb=" N LEU P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 85 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA P 89 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA P 96 " --> pdb=" O THR P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 44 removed outlier: 3.754A pdb=" N ILE Q 37 " --> pdb=" O GLY Q 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 67 removed outlier: 4.089A pdb=" N ILE Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY Q 52 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 98 removed outlier: 3.907A pdb=" N LEU Q 74 " --> pdb=" O MET Q 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU Q 75 " --> pdb=" O SER Q 71 " (cutoff:3.500A) Proline residue: Q 76 - end of helix removed outlier: 3.633A pdb=" N PHE Q 82 " --> pdb=" O CYS Q 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU Q 84 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA Q 87 " --> pdb=" O ALA Q 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.799A pdb=" N GLY R 38 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 47 removed outlier: 4.113A pdb=" N GLY R 47 " --> pdb=" O SER R 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 44 through 47' Processing helix chain 'R' and resid 49 through 67 Processing helix chain 'R' and resid 70 through 99 removed outlier: 4.051A pdb=" N LEU R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 3.627A pdb=" N SER R 85 " --> pdb=" O GLY R 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 44 removed outlier: 4.098A pdb=" N ALA S 39 " --> pdb=" O ASN S 35 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 67 removed outlier: 4.077A pdb=" N ILE S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY S 52 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 71 Processing helix chain 'S' and resid 75 through 99 removed outlier: 4.124A pdb=" N GLY S 81 " --> pdb=" O TYR S 77 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU S 84 " --> pdb=" O LEU S 80 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER S 85 " --> pdb=" O GLY S 81 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE S 95 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 36 Processing helix chain 'T' and resid 37 through 47 removed outlier: 3.637A pdb=" N MET T 41 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY T 47 " --> pdb=" O ALA T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 67 removed outlier: 4.018A pdb=" N GLY T 52 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER T 59 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU T 62 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 71 Processing helix chain 'T' and resid 74 through 99 removed outlier: 3.602A pdb=" N ALA T 89 " --> pdb=" O SER T 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 36 Processing helix chain 'U' and resid 37 through 44 Processing helix chain 'U' and resid 47 through 67 removed outlier: 3.819A pdb=" N ILE U 51 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY U 52 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 99 Proline residue: U 76 - end of helix removed outlier: 4.004A pdb=" N SER U 85 " --> pdb=" O GLY U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 44 removed outlier: 4.254A pdb=" N GLY V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA V 39 " --> pdb=" O ASN V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 67 removed outlier: 4.094A pdb=" N ILE V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY V 52 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 75 removed outlier: 3.918A pdb=" N LEU V 75 " --> pdb=" O SER V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 99 removed outlier: 3.917A pdb=" N GLY V 81 " --> pdb=" O TYR V 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER V 85 " --> pdb=" O GLY V 81 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA V 89 " --> pdb=" O SER V 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR V 92 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 44 removed outlier: 3.614A pdb=" N ILE W 37 " --> pdb=" O GLY W 33 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA W 39 " --> pdb=" O ASN W 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 47 No H-bonds generated for 'chain 'W' and resid 45 through 47' Processing helix chain 'W' and resid 48 through 67 removed outlier: 3.972A pdb=" N GLY W 52 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS W 56 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 71 Processing helix chain 'W' and resid 74 through 99 Processing helix chain 'X' and resid 33 through 44 removed outlier: 3.673A pdb=" N ILE X 37 " --> pdb=" O GLY X 33 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY X 38 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA X 39 " --> pdb=" O ASN X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 67 removed outlier: 4.273A pdb=" N ILE X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY X 52 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR X 60 " --> pdb=" O CYS X 56 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU X 62 " --> pdb=" O SER X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 75 removed outlier: 3.792A pdb=" N LEU X 75 " --> pdb=" O SER X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 98 removed outlier: 4.238A pdb=" N GLY X 81 " --> pdb=" O TYR X 77 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE X 95 " --> pdb=" O PHE X 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) Processing helix chain '0' and resid 142 through 167 removed outlier: 3.860A pdb=" N GLU 0 147 " --> pdb=" O LYS 0 143 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL 0 150 " --> pdb=" O GLN 0 146 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR 0 165 " --> pdb=" O GLU 0 161 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET 0 166 " --> pdb=" O TRP 0 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 73 through 77 removed outlier: 6.789A pdb=" N LEU G 74 " --> pdb=" O GLN G 158 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL G 160 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL G 76 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASN G 162 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP H 25 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 106 through 107 removed outlier: 7.747A pdb=" N ILE G 106 " --> pdb=" O ARG G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AA4, first strand: chain 'H' and resid 57 through 64 removed outlier: 5.885A pdb=" N LYS H 60 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU H 51 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE H 48 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE H 123 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR H 50 " --> pdb=" O ILE H 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.282A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'O' and resid 25 through 31 removed outlier: 6.125A pdb=" N ILE P 25 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR Q 30 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR P 27 " --> pdb=" O THR Q 30 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA O 26 " --> pdb=" O ILE X 25 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N TYR X 27 " --> pdb=" O ALA O 26 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU O 28 " --> pdb=" O TYR X 27 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL X 29 " --> pdb=" O GLU O 28 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR O 30 " --> pdb=" O VAL X 29 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL X 31 " --> pdb=" O THR O 30 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1878 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: 7.26 Time building geometry restraints manager: 16.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10242 1.03 - 1.22: 35 1.22 - 1.42: 4110 1.42 - 1.61: 5960 1.61 - 1.81: 130 Bond restraints: 20477 Sorted by residual: bond pdb=" CG LEU P 100 " pdb=" CD2 LEU P 100 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.89e+00 bond pdb=" CB THR G 31 " pdb=" CG2 THR G 31 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.22e+00 bond pdb=" CG LEU X 100 " pdb=" CD2 LEU X 100 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CB VAL X 29 " pdb=" CG2 VAL X 29 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.55e+00 bond pdb=" CB CYS U 56 " pdb=" SG CYS U 56 " ideal model delta sigma weight residual 1.808 1.747 0.061 3.30e-02 9.18e+02 3.37e+00 ... (remaining 20472 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.24: 179 104.24 - 111.71: 23559 111.71 - 119.18: 5124 119.18 - 126.65: 8180 126.65 - 134.12: 84 Bond angle restraints: 37126 Sorted by residual: angle pdb=" N VAL G 99 " pdb=" CA VAL G 99 " pdb=" CB VAL G 99 " ideal model delta sigma weight residual 112.15 106.10 6.05 1.47e+00 4.63e-01 1.69e+01 angle pdb=" C VAL Q 48 " pdb=" CA VAL Q 48 " pdb=" CB VAL Q 48 " ideal model delta sigma weight residual 114.35 110.68 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" N LEU X 36 " pdb=" CA LEU X 36 " pdb=" CB LEU X 36 " ideal model delta sigma weight residual 110.51 104.67 5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" C GLY Q 47 " pdb=" N VAL Q 48 " pdb=" CA VAL Q 48 " ideal model delta sigma weight residual 120.24 122.35 -2.11 6.30e-01 2.52e+00 1.12e+01 angle pdb=" N LEU O 36 " pdb=" CA LEU O 36 " pdb=" CB LEU O 36 " ideal model delta sigma weight residual 110.51 105.39 5.12 1.70e+00 3.46e-01 9.08e+00 ... (remaining 37121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 8193 15.60 - 31.20: 1041 31.20 - 46.80: 274 46.80 - 62.40: 119 62.40 - 78.00: 4 Dihedral angle restraints: 9631 sinusoidal: 5171 harmonic: 4460 Sorted by residual: dihedral pdb=" CA ASN T 35 " pdb=" C ASN T 35 " pdb=" N LEU T 36 " pdb=" CA LEU T 36 " ideal model delta harmonic sigma weight residual 180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA ASN V 35 " pdb=" C ASN V 35 " pdb=" N LEU V 36 " pdb=" CA LEU V 36 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASN U 35 " pdb=" C ASN U 35 " pdb=" N LEU U 36 " pdb=" CA LEU U 36 " ideal model delta harmonic sigma weight residual -180.00 -154.24 -25.76 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 9628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1013 0.039 - 0.077: 415 0.077 - 0.116: 170 0.116 - 0.155: 42 0.155 - 0.194: 8 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB VAL T 29 " pdb=" CA VAL T 29 " pdb=" CG1 VAL T 29 " pdb=" CG2 VAL T 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CB THR G 268 " pdb=" CA THR G 268 " pdb=" OG1 THR G 268 " pdb=" CG2 THR G 268 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA VAL G 152 " pdb=" N VAL G 152 " pdb=" C VAL G 152 " pdb=" CB VAL G 152 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 1645 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 48 " 0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO P 49 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO P 49 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 49 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL S 48 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO S 49 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO S 49 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 49 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 75 " 0.039 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO R 76 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 76 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 76 " 0.033 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3108 2.27 - 2.85: 47755 2.85 - 3.44: 53319 3.44 - 4.02: 73892 4.02 - 4.60: 115916 Nonbonded interactions: 293990 Sorted by model distance: nonbonded pdb="HD22 ASN Q 35 " pdb=" O PHE Q 103 " model vdw 1.689 1.850 nonbonded pdb=" OD1 ASP G 46 " pdb="HH22 ARG G 163 " model vdw 1.696 1.850 nonbonded pdb="HD22 ASN O 35 " pdb=" O PHE O 103 " model vdw 1.711 1.850 nonbonded pdb=" OE1 GLU H 144 " pdb=" H GLU H 144 " model vdw 1.714 1.850 nonbonded pdb=" HH TYR T 60 " pdb=" O SER T 71 " model vdw 1.716 1.850 ... (remaining 293985 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.630 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: 0.310 Extract box with map and model: 19.550 Check model and map are aligned: 0.320 Set scattering table: 0.220 Process input model: 65.830 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.010 0.073 10211 Z= 0.666 Angle : 0.874 9.276 13840 Z= 0.456 Chirality : 0.050 0.194 1648 Planarity : 0.007 0.067 1744 Dihedral : 13.706 71.402 3621 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % 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: -3.55 (0.20), residues: 1311 helix: -2.00 (0.15), residues: 807 sheet: -4.07 (0.38), residues: 87 loop : -2.26 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 154 HIS 0.006 0.002 HIS H 82 PHE 0.029 0.002 PHE H 57 TYR 0.017 0.002 TYR I 46 ARG 0.004 0.001 ARG V 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 ILE cc_start: 0.8423 (mt) cc_final: 0.8211 (mm) REVERT: T 46 VAL cc_start: 0.8637 (t) cc_final: 0.8396 (t) REVERT: U 73 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7523 (mptt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.5071 time to fit residues: 133.8397 Evaluate side-chains 128 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 204 GLN ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN V 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10211 Z= 0.325 Angle : 0.680 9.100 13840 Z= 0.344 Chirality : 0.040 0.136 1648 Planarity : 0.005 0.055 1744 Dihedral : 4.950 21.888 1413 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.64 % Allowed : 11.51 % Favored : 86.85 % 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: -2.02 (0.22), residues: 1311 helix: -0.48 (0.17), residues: 856 sheet: -3.93 (0.38), residues: 92 loop : -2.43 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 42 HIS 0.006 0.001 HIS H 114 PHE 0.020 0.002 PHE V 82 TYR 0.017 0.002 TYR W 60 ARG 0.002 0.000 ARG V 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6670 (mtt) REVERT: G 259 THR cc_start: 0.7217 (p) cc_final: 0.6965 (p) REVERT: Q 66 ARG cc_start: 0.7738 (tpt90) cc_final: 0.7183 (tpt-90) REVERT: U 73 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7784 (mptt) outliers start: 17 outliers final: 9 residues processed: 180 average time/residue: 0.5424 time to fit residues: 136.6400 Evaluate side-chains 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain V residue 67 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN H 160 GLN R 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10211 Z= 0.311 Angle : 0.617 8.431 13840 Z= 0.313 Chirality : 0.040 0.142 1648 Planarity : 0.005 0.055 1744 Dihedral : 4.605 18.610 1413 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.74 % Allowed : 13.73 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1311 helix: 0.25 (0.18), residues: 857 sheet: -3.55 (0.41), residues: 87 loop : -2.14 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 154 HIS 0.005 0.001 HIS H 114 PHE 0.017 0.002 PHE U 103 TYR 0.012 0.002 TYR W 77 ARG 0.007 0.000 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6931 (mtt) REVERT: I 64 LYS cc_start: 0.8119 (mttt) cc_final: 0.7890 (mtpt) REVERT: Q 66 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7234 (tpt-90) REVERT: T 61 MET cc_start: 0.7931 (mtt) cc_final: 0.7704 (mtt) REVERT: U 55 MET cc_start: 0.7753 (ttm) cc_final: 0.7518 (ttm) REVERT: U 73 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7905 (mptt) outliers start: 18 outliers final: 8 residues processed: 180 average time/residue: 0.5508 time to fit residues: 136.7330 Evaluate side-chains 155 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain 0 residue 166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10211 Z= 0.253 Angle : 0.576 8.667 13840 Z= 0.291 Chirality : 0.039 0.147 1648 Planarity : 0.005 0.048 1744 Dihedral : 4.343 16.695 1413 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.74 % Allowed : 15.57 % Favored : 82.69 % 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: -0.59 (0.24), residues: 1311 helix: 0.62 (0.18), residues: 863 sheet: -3.40 (0.42), residues: 87 loop : -1.94 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 154 HIS 0.005 0.001 HIS G 227 PHE 0.013 0.001 PHE V 82 TYR 0.011 0.002 TYR P 60 ARG 0.005 0.000 ARG P 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 189 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: G 259 THR cc_start: 0.7153 (p) cc_final: 0.6816 (p) REVERT: H 60 LYS cc_start: 0.8300 (tttt) cc_final: 0.8018 (ttpp) REVERT: Q 66 ARG cc_start: 0.7839 (tpt90) cc_final: 0.7292 (tpt-90) REVERT: S 35 ASN cc_start: 0.8020 (t0) cc_final: 0.7782 (t0) REVERT: U 55 MET cc_start: 0.7844 (ttm) cc_final: 0.7593 (ttm) REVERT: U 73 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7861 (mptt) REVERT: U 74 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8214 (mt) outliers start: 18 outliers final: 13 residues processed: 172 average time/residue: 0.5492 time to fit residues: 131.7661 Evaluate side-chains 167 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain 0 residue 166 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN H 136 HIS ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10211 Z= 0.303 Angle : 0.585 8.924 13840 Z= 0.298 Chirality : 0.040 0.145 1648 Planarity : 0.005 0.048 1744 Dihedral : 4.259 18.233 1413 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.19 % Allowed : 15.38 % Favored : 81.43 % 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: -0.34 (0.24), residues: 1311 helix: 0.79 (0.18), residues: 864 sheet: -3.18 (0.45), residues: 87 loop : -1.83 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 154 HIS 0.006 0.001 HIS G 227 PHE 0.012 0.001 PHE G 223 TYR 0.012 0.002 TYR W 77 ARG 0.009 0.000 ARG P 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 66 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7289 (tpt-90) REVERT: U 55 MET cc_start: 0.7973 (ttm) cc_final: 0.7726 (ttm) REVERT: U 73 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7921 (mptt) REVERT: U 74 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8258 (mt) REVERT: W 71 SER cc_start: 0.8734 (t) cc_final: 0.8364 (p) REVERT: W 99 GLU cc_start: 0.8484 (tt0) cc_final: 0.7863 (tt0) outliers start: 33 outliers final: 21 residues processed: 194 average time/residue: 0.5342 time to fit residues: 146.7821 Evaluate side-chains 183 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 55 MET Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain 0 residue 166 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10211 Z= 0.288 Angle : 0.572 8.784 13840 Z= 0.292 Chirality : 0.039 0.139 1648 Planarity : 0.004 0.051 1744 Dihedral : 4.202 17.612 1413 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.00 % Allowed : 16.54 % Favored : 80.46 % 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: -0.21 (0.24), residues: 1311 helix: 0.90 (0.18), residues: 867 sheet: -2.94 (0.48), residues: 87 loop : -1.88 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 154 HIS 0.006 0.001 HIS G 227 PHE 0.017 0.001 PHE Q 57 TYR 0.011 0.002 TYR V 60 ARG 0.004 0.000 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.466 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: G 34 LYS cc_start: 0.8560 (tttt) cc_final: 0.8181 (ttmt) REVERT: P 66 ARG cc_start: 0.7699 (mtp85) cc_final: 0.7298 (mtt90) REVERT: Q 66 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7263 (tpt-90) REVERT: U 55 MET cc_start: 0.8013 (ttm) cc_final: 0.7793 (ttm) REVERT: U 73 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7932 (mptt) REVERT: U 74 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (mt) REVERT: U 91 PHE cc_start: 0.8013 (m-10) cc_final: 0.7793 (m-80) REVERT: W 71 SER cc_start: 0.8746 (t) cc_final: 0.8433 (p) REVERT: W 99 GLU cc_start: 0.8513 (tt0) cc_final: 0.7933 (tt0) outliers start: 31 outliers final: 25 residues processed: 184 average time/residue: 0.5389 time to fit residues: 139.1241 Evaluate side-chains 184 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 82 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain 0 residue 166 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 126 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10211 Z= 0.253 Angle : 0.559 8.485 13840 Z= 0.283 Chirality : 0.039 0.156 1648 Planarity : 0.004 0.063 1744 Dihedral : 4.110 18.557 1413 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.71 % Allowed : 17.99 % Favored : 79.30 % 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: 0.04 (0.24), residues: 1311 helix: 1.07 (0.18), residues: 863 sheet: -2.85 (0.50), residues: 87 loop : -1.70 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 154 HIS 0.005 0.001 HIS G 227 PHE 0.012 0.001 PHE G 223 TYR 0.010 0.002 TYR X 27 ARG 0.013 0.000 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.532 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: G 34 LYS cc_start: 0.8545 (tttt) cc_final: 0.8162 (ttmt) REVERT: G 125 TYR cc_start: 0.8737 (t80) cc_final: 0.8001 (t80) REVERT: I 64 LYS cc_start: 0.8113 (mttt) cc_final: 0.7870 (mtpt) REVERT: O 51 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8223 (mt) REVERT: Q 66 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7285 (tpt-90) REVERT: U 55 MET cc_start: 0.8034 (ttm) cc_final: 0.7818 (ttm) REVERT: U 73 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7938 (mptt) REVERT: U 74 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8233 (mt) REVERT: W 71 SER cc_start: 0.8704 (t) cc_final: 0.8431 (p) REVERT: W 99 GLU cc_start: 0.8435 (tt0) cc_final: 0.7961 (tt0) outliers start: 28 outliers final: 24 residues processed: 184 average time/residue: 0.5345 time to fit residues: 136.6787 Evaluate side-chains 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 82 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10211 Z= 0.233 Angle : 0.541 8.397 13840 Z= 0.274 Chirality : 0.038 0.137 1648 Planarity : 0.004 0.050 1744 Dihedral : 4.007 16.267 1413 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.71 % Allowed : 18.28 % Favored : 79.01 % 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: 0.18 (0.24), residues: 1311 helix: 1.18 (0.18), residues: 868 sheet: -2.70 (0.51), residues: 87 loop : -1.71 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 154 HIS 0.005 0.001 HIS G 227 PHE 0.012 0.001 PHE G 223 TYR 0.011 0.001 TYR X 27 ARG 0.002 0.000 ARG G 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.628 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: G 125 TYR cc_start: 0.8747 (t80) cc_final: 0.7901 (t80) REVERT: H 47 ILE cc_start: 0.8727 (pt) cc_final: 0.8460 (mt) REVERT: Q 66 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7299 (tpt-90) REVERT: U 55 MET cc_start: 0.8034 (ttm) cc_final: 0.7824 (ttm) REVERT: U 74 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (mt) REVERT: W 99 GLU cc_start: 0.8424 (tt0) cc_final: 0.7970 (tt0) outliers start: 28 outliers final: 25 residues processed: 190 average time/residue: 0.5020 time to fit residues: 133.1834 Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain O residue 82 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10211 Z= 0.303 Angle : 0.577 8.878 13840 Z= 0.295 Chirality : 0.040 0.181 1648 Planarity : 0.005 0.068 1744 Dihedral : 4.098 19.179 1413 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.71 % Allowed : 17.99 % Favored : 79.30 % 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: 0.19 (0.24), residues: 1311 helix: 1.17 (0.18), residues: 864 sheet: -2.73 (0.50), residues: 87 loop : -1.62 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 154 HIS 0.006 0.002 HIS G 227 PHE 0.013 0.001 PHE G 223 TYR 0.012 0.002 TYR V 60 ARG 0.011 0.000 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.691 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: G 125 TYR cc_start: 0.8760 (t80) cc_final: 0.7927 (t80) REVERT: H 47 ILE cc_start: 0.8785 (pt) cc_final: 0.8494 (mt) REVERT: Q 66 ARG cc_start: 0.7932 (tpt90) cc_final: 0.7306 (tpt-90) REVERT: U 74 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8241 (mt) REVERT: W 99 GLU cc_start: 0.8480 (tt0) cc_final: 0.8045 (tt0) REVERT: X 73 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8167 (ttmt) outliers start: 28 outliers final: 25 residues processed: 184 average time/residue: 0.5181 time to fit residues: 132.3944 Evaluate side-chains 186 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain O residue 82 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 35 ASN Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 0.0980 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10211 Z= 0.215 Angle : 0.537 8.186 13840 Z= 0.272 Chirality : 0.038 0.135 1648 Planarity : 0.004 0.051 1744 Dihedral : 3.965 16.942 1413 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.42 % Allowed : 17.89 % Favored : 79.69 % 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: 0.35 (0.24), residues: 1311 helix: 1.32 (0.18), residues: 868 sheet: -2.57 (0.51), residues: 87 loop : -1.70 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 183 HIS 0.005 0.001 HIS G 227 PHE 0.011 0.001 PHE G 223 TYR 0.011 0.001 TYR X 27 ARG 0.002 0.000 ARG G 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2622 Ramachandran restraints generated. 1311 Oldfield, 0 Emsley, 1311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7190 (ttp80) REVERT: G 125 TYR cc_start: 0.8735 (t80) cc_final: 0.7910 (t80) REVERT: H 47 ILE cc_start: 0.8785 (pt) cc_final: 0.8501 (mt) REVERT: Q 66 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7299 (tpt-90) REVERT: U 46 VAL cc_start: 0.9149 (t) cc_final: 0.8927 (t) REVERT: U 74 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8204 (mt) REVERT: V 99 GLU cc_start: 0.8261 (tt0) cc_final: 0.8017 (tt0) REVERT: W 99 GLU cc_start: 0.8381 (tt0) cc_final: 0.7950 (tt0) outliers start: 25 outliers final: 24 residues processed: 187 average time/residue: 0.5258 time to fit residues: 138.9118 Evaluate side-chains 189 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 CYS Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 82 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 67 GLN Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 239 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 = 0.3287 r_free = 0.3287 target = 0.109061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097235 restraints weight = 39851.658| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.60 r_work: 0.3201 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10211 Z= 0.236 Angle : 0.544 8.280 13840 Z= 0.276 Chirality : 0.038 0.149 1648 Planarity : 0.004 0.065 1744 Dihedral : 3.958 17.457 1413 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.61 % Allowed : 18.18 % Favored : 79.21 % 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: 0.42 (0.24), residues: 1311 helix: 1.38 (0.18), residues: 868 sheet: -2.58 (0.51), residues: 87 loop : -1.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 183 HIS 0.005 0.001 HIS G 227 PHE 0.012 0.001 PHE G 223 TYR 0.011 0.001 TYR X 27 ARG 0.010 0.000 ARG G 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4952.35 seconds wall clock time: 88 minutes 55.11 seconds (5335.11 seconds total)