Starting phenix.real_space_refine on Thu Sep 18 20:46:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_10470.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_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 { model { file = "/net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_10470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_10470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_10470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tdx_10470/09_2025/6tdx_10470.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.81, per 1000 atoms: 0.19 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 - 3.00 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: 2.00 Conformation dependent library (CDL) restraints added in 542.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.52 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: 4.70 Time building geometry restraints manager: 2.62 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: 0.00 - 1.86: 35921 1.86 - 3.71: 1070 3.71 - 5.57: 103 5.57 - 7.42: 23 7.42 - 9.28: 9 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 2.450 nonbonded pdb=" OD1 ASP G 46 " pdb="HH22 ARG G 163 " model vdw 1.696 2.450 nonbonded pdb="HD22 ASN O 35 " pdb=" O PHE O 103 " model vdw 1.711 2.450 nonbonded pdb=" OE1 GLU H 144 " pdb=" H GLU H 144 " model vdw 1.714 2.450 nonbonded pdb=" HH TYR T 60 " pdb=" O SER T 71 " model vdw 1.716 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 5.780 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: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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= 0.399 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG V 66 TYR 0.017 0.002 TYR I 46 PHE 0.029 0.002 PHE H 57 TRP 0.006 0.001 TRP G 154 HIS 0.006 0.002 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.01022 (10211) covalent geometry : angle 0.87396 (13840) hydrogen bonds : bond 0.17542 ( 648) hydrogen bonds : angle 7.89661 ( 1878) *********************** 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 to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.555 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: 0.8212 (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: 0.7524 (mptt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2403 time to fit residues: 63.1525 Evaluate side-chains 126 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 H 72 ASN T 69 ASN U 69 ASN V 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124573 restraints weight = 34945.046| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.55 r_work: 0.3406 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10211 Z= 0.161 Angle : 0.635 7.718 13840 Z= 0.322 Chirality : 0.039 0.137 1648 Planarity : 0.006 0.052 1744 Dihedral : 4.949 21.616 1413 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.97 % Allowed : 11.70 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.22), residues: 1311 helix: -0.43 (0.17), residues: 853 sheet: -3.82 (0.41), residues: 86 loop : -2.45 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 41 TYR 0.012 0.001 TYR I 13 PHE 0.019 0.001 PHE V 82 TRP 0.004 0.000 TRP G 154 HIS 0.004 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00343 (10211) covalent geometry : angle 0.63476 (13840) hydrogen bonds : bond 0.05671 ( 648) hydrogen bonds : angle 5.24869 ( 1878) *********************** 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 162 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.459 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 137 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6851 (mtt) REVERT: G 208 MET cc_start: 0.8442 (tpt) cc_final: 0.8211 (tpt) REVERT: H 21 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7946 (mtpp) REVERT: S 85 SER cc_start: 0.8876 (t) cc_final: 0.8603 (m) REVERT: T 35 ASN cc_start: 0.7884 (t0) cc_final: 0.7600 (t0) REVERT: T 46 VAL cc_start: 0.8392 (t) cc_final: 0.8122 (t) REVERT: U 73 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7620 (mptt) outliers start: 10 outliers final: 8 residues processed: 157 average time/residue: 0.2256 time to fit residues: 50.6153 Evaluate side-chains 142 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 32 ASP Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain V residue 67 GLN Chi-restraints excluded: chain W residue 35 ASN Chi-restraints excluded: chain W residue 36 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115531 restraints weight = 36696.030| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.56 r_work: 0.3322 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2621 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= 0.168 Angle : 0.585 8.430 13840 Z= 0.296 Chirality : 0.039 0.138 1648 Planarity : 0.005 0.051 1744 Dihedral : 4.465 18.082 1413 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.74 % Allowed : 12.96 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.23), residues: 1311 helix: 0.45 (0.18), residues: 853 sheet: -3.71 (0.41), residues: 92 loop : -2.13 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 53 TYR 0.012 0.002 TYR I 13 PHE 0.013 0.001 PHE V 82 TRP 0.004 0.001 TRP 0 162 HIS 0.005 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00374 (10211) covalent geometry : angle 0.58516 (13840) hydrogen bonds : bond 0.04677 ( 648) hydrogen bonds : angle 4.63792 ( 1878) *********************** 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 180 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8373 (mttt) cc_final: 0.8119 (mttm) REVERT: G 137 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7110 (mtt) REVERT: H 21 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8036 (mtpp) REVERT: Q 66 ARG cc_start: 0.7910 (tpt90) cc_final: 0.7374 (tpt-90) REVERT: S 53 VAL cc_start: 0.8081 (t) cc_final: 0.7866 (p) REVERT: S 85 SER cc_start: 0.8907 (t) cc_final: 0.8396 (m) REVERT: T 35 ASN cc_start: 0.7804 (t0) cc_final: 0.7555 (t0) REVERT: T 46 VAL cc_start: 0.8323 (t) cc_final: 0.7998 (t) REVERT: U 73 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7891 (mptt) outliers start: 18 outliers final: 6 residues processed: 171 average time/residue: 0.2538 time to fit residues: 61.0720 Evaluate side-chains 150 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain V residue 67 GLN 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 34 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 176 ASN H 160 GLN W 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111792 restraints weight = 37729.611| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.60 r_work: 0.3254 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3264 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= 0.183 Angle : 0.577 8.699 13840 Z= 0.293 Chirality : 0.039 0.133 1648 Planarity : 0.005 0.052 1744 Dihedral : 4.263 16.316 1413 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.03 % Allowed : 15.38 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1311 helix: 0.71 (0.18), residues: 858 sheet: -3.37 (0.45), residues: 87 loop : -1.92 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 163 TYR 0.012 0.002 TYR P 77 PHE 0.013 0.001 PHE V 82 TRP 0.003 0.001 TRP 0 162 HIS 0.005 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00411 (10211) covalent geometry : angle 0.57703 (13840) hydrogen bonds : bond 0.04549 ( 648) hydrogen bonds : angle 4.37271 ( 1878) *********************** 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 183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.507 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: 0.7763 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: G 266 ASP cc_start: 0.7700 (t70) cc_final: 0.7484 (t0) REVERT: H 21 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8093 (mtpp) REVERT: Q 66 ARG cc_start: 0.7978 (tpt90) cc_final: 0.7465 (tpt-90) REVERT: S 53 VAL cc_start: 0.8152 (t) cc_final: 0.7950 (t) REVERT: S 85 SER cc_start: 0.8990 (t) cc_final: 0.8567 (m) REVERT: T 35 ASN cc_start: 0.7785 (t0) cc_final: 0.7537 (t0) REVERT: T 71 SER cc_start: 0.8753 (t) cc_final: 0.8481 (p) REVERT: U 73 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7891 (mptt) REVERT: V 99 GLU cc_start: 0.8477 (tt0) cc_final: 0.8235 (tt0) outliers start: 21 outliers final: 11 residues processed: 173 average time/residue: 0.2215 time to fit residues: 53.7951 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain V residue 67 GLN 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 40 optimal weight: 0.9980 chunk 112 optimal weight: 0.0000 chunk 6 optimal weight: 0.0060 chunk 20 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 HIS I 25 GLN W 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114339 restraints weight = 37137.134| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.60 r_work: 0.3285 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10211 Z= 0.115 Angle : 0.516 7.832 13840 Z= 0.261 Chirality : 0.037 0.132 1648 Planarity : 0.004 0.053 1744 Dihedral : 4.021 14.962 1413 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.06 % Allowed : 16.73 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.24), residues: 1311 helix: 1.15 (0.18), residues: 857 sheet: -3.17 (0.47), residues: 86 loop : -1.76 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 66 TYR 0.010 0.001 TYR X 27 PHE 0.012 0.001 PHE V 82 TRP 0.002 0.000 TRP I 3 HIS 0.004 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00239 (10211) covalent geometry : angle 0.51584 (13840) hydrogen bonds : bond 0.04166 ( 648) hydrogen bonds : angle 4.11181 ( 1878) *********************** 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 166 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.551 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: 0.7591 (mtt) cc_final: 0.7173 (mtt) REVERT: G 259 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7208 (p) REVERT: H 21 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8024 (mtpp) REVERT: I 64 LYS cc_start: 0.8196 (mttt) cc_final: 0.7968 (mtpt) REVERT: Q 66 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7481 (tpt-90) REVERT: T 35 ASN cc_start: 0.7678 (t0) cc_final: 0.7415 (t0) REVERT: T 71 SER cc_start: 0.8852 (t) cc_final: 0.8522 (p) REVERT: U 73 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7914 (mptt) outliers start: 11 outliers final: 6 residues processed: 160 average time/residue: 0.2706 time to fit residues: 59.3632 Evaluate side-chains 153 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 208 MET Chi-restraints excluded: chain G residue 259 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain V residue 67 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 50 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN ** S 35 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 = 0.3411 r_free = 0.3411 target = 0.116661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104635 restraints weight = 39040.210| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.60 r_work: 0.3250 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10211 Z= 0.145 Angle : 0.525 8.357 13840 Z= 0.267 Chirality : 0.038 0.134 1648 Planarity : 0.004 0.053 1744 Dihedral : 3.940 14.607 1413 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.45 % Allowed : 17.02 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.24), residues: 1311 helix: 1.32 (0.18), residues: 864 sheet: -3.03 (0.48), residues: 87 loop : -1.71 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 66 TYR 0.011 0.001 TYR I 13 PHE 0.012 0.001 PHE G 223 TRP 0.002 0.000 TRP 0 162 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00322 (10211) covalent geometry : angle 0.52517 (13840) hydrogen bonds : bond 0.04132 ( 648) hydrogen bonds : angle 4.05126 ( 1878) *********************** 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 172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8237 (tppp) REVERT: H 21 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8070 (mtpp) REVERT: H 87 GLN cc_start: 0.8093 (pt0) cc_final: 0.7743 (mt0) REVERT: I 64 LYS cc_start: 0.8176 (mttt) cc_final: 0.7965 (mtpt) REVERT: P 66 ARG cc_start: 0.7723 (mtt90) cc_final: 0.7484 (mtt-85) REVERT: Q 66 ARG cc_start: 0.8030 (tpt90) cc_final: 0.7469 (tpt-90) REVERT: S 41 MET cc_start: 0.8015 (tpp) cc_final: 0.7799 (mtm) REVERT: T 35 ASN cc_start: 0.7733 (t0) cc_final: 0.7473 (t0) REVERT: T 71 SER cc_start: 0.8880 (t) cc_final: 0.8562 (p) REVERT: U 73 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7891 (mptt) REVERT: W 99 GLU cc_start: 0.8733 (tt0) cc_final: 0.8275 (tt0) outliers start: 15 outliers final: 11 residues processed: 168 average time/residue: 0.2413 time to fit residues: 56.7370 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain Q residue 44 SER Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 104 SER Chi-restraints excluded: chain U residue 82 PHE Chi-restraints excluded: chain V residue 67 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 GLN ** S 35 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 = 0.3394 r_free = 0.3394 target = 0.115216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103093 restraints weight = 39712.610| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.62 r_work: 0.3213 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4128 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= 0.177 Angle : 0.546 8.586 13840 Z= 0.279 Chirality : 0.039 0.137 1648 Planarity : 0.004 0.053 1744 Dihedral : 3.969 14.814 1413 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.84 % Allowed : 16.83 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.24), residues: 1311 helix: 1.34 (0.18), residues: 864 sheet: -3.09 (0.48), residues: 87 loop : -1.65 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 66 TYR 0.012 0.002 TYR I 13 PHE 0.013 0.001 PHE G 223 TRP 0.003 0.001 TRP I 3 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00404 (10211) covalent geometry : angle 0.54616 (13840) hydrogen bonds : bond 0.04273 ( 648) hydrogen bonds : angle 4.04387 ( 1878) *********************** 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 183 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8252 (tppp) REVERT: H 60 LYS cc_start: 0.8554 (tttt) cc_final: 0.8083 (ttpp) REVERT: H 87 GLN cc_start: 0.8090 (pt0) cc_final: 0.7781 (mt0) REVERT: P 66 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7500 (mtt-85) REVERT: Q 66 ARG cc_start: 0.8086 (tpt90) cc_final: 0.7534 (tpt-90) REVERT: S 59 SER cc_start: 0.9076 (p) cc_final: 0.8858 (p) REVERT: S 85 SER cc_start: 0.9000 (t) cc_final: 0.8482 (m) REVERT: T 71 SER cc_start: 0.8853 (t) cc_final: 0.8568 (p) REVERT: U 73 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7933 (mptt) REVERT: W 99 GLU cc_start: 0.8812 (tt0) cc_final: 0.8309 (tt0) outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 0.2380 time to fit residues: 59.5865 Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain T residue 104 SER 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 0 residue 166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN R 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103892 restraints weight = 39562.700| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.62 r_work: 0.3205 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10211 Z= 0.161 Angle : 0.533 8.388 13840 Z= 0.271 Chirality : 0.038 0.135 1648 Planarity : 0.004 0.054 1744 Dihedral : 3.911 15.030 1413 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.64 % Allowed : 17.41 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1311 helix: 1.44 (0.18), residues: 864 sheet: -3.05 (0.48), residues: 87 loop : -1.58 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 66 TYR 0.010 0.001 TYR X 27 PHE 0.013 0.001 PHE G 223 TRP 0.002 0.000 TRP G 183 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00364 (10211) covalent geometry : angle 0.53259 (13840) hydrogen bonds : bond 0.04181 ( 648) hydrogen bonds : angle 4.00388 ( 1878) *********************** 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 179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8249 (tppp) REVERT: H 60 LYS cc_start: 0.8531 (tttt) cc_final: 0.8042 (ttpp) REVERT: H 87 GLN cc_start: 0.8046 (pt0) cc_final: 0.7756 (mt0) REVERT: P 66 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7477 (mtt-85) REVERT: Q 66 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7513 (tpt-90) REVERT: S 59 SER cc_start: 0.9127 (p) cc_final: 0.8900 (p) REVERT: S 85 SER cc_start: 0.8980 (t) cc_final: 0.8539 (m) REVERT: T 41 MET cc_start: 0.7449 (mtp) cc_final: 0.7245 (mtt) REVERT: T 71 SER cc_start: 0.8815 (t) cc_final: 0.8484 (p) REVERT: U 73 LYS cc_start: 0.8395 (mtpt) cc_final: 0.7938 (mptt) REVERT: W 71 SER cc_start: 0.8962 (t) cc_final: 0.8526 (p) REVERT: W 99 GLU cc_start: 0.8766 (tt0) cc_final: 0.8273 (tt0) outliers start: 17 outliers final: 16 residues processed: 172 average time/residue: 0.2446 time to fit residues: 58.7122 Evaluate side-chains 173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 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 35 ASN Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain 0 residue 166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 GLN G 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102943 restraints weight = 39751.149| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.60 r_work: 0.3168 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10211 Z= 0.183 Angle : 0.550 8.623 13840 Z= 0.281 Chirality : 0.039 0.136 1648 Planarity : 0.004 0.054 1744 Dihedral : 3.960 15.619 1413 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.84 % Allowed : 17.50 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1311 helix: 1.41 (0.18), residues: 868 sheet: -3.07 (0.48), residues: 87 loop : -1.70 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 66 TYR 0.010 0.002 TYR W 60 PHE 0.013 0.001 PHE G 223 TRP 0.001 0.000 TRP I 42 HIS 0.006 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00418 (10211) covalent geometry : angle 0.55006 (13840) hydrogen bonds : bond 0.04261 ( 648) hydrogen bonds : angle 4.03569 ( 1878) *********************** 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 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8257 (tppp) REVERT: G 82 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7334 (ttp80) REVERT: H 21 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8216 (mtpp) REVERT: H 60 LYS cc_start: 0.8509 (tttt) cc_final: 0.8022 (ttpp) REVERT: H 87 GLN cc_start: 0.8027 (pt0) cc_final: 0.7754 (mt0) REVERT: P 66 ARG cc_start: 0.7733 (mtt90) cc_final: 0.7413 (mtt-85) REVERT: P 70 MET cc_start: 0.8192 (mmp) cc_final: 0.7626 (mmt) REVERT: Q 66 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7488 (tpt-90) REVERT: S 59 SER cc_start: 0.9143 (p) cc_final: 0.8909 (p) REVERT: S 85 SER cc_start: 0.8988 (t) cc_final: 0.8626 (m) REVERT: T 41 MET cc_start: 0.7533 (mtp) cc_final: 0.7326 (mtt) REVERT: T 71 SER cc_start: 0.8864 (t) cc_final: 0.8538 (p) REVERT: W 69 ASN cc_start: 0.8239 (m-40) cc_final: 0.7929 (m-40) REVERT: W 71 SER cc_start: 0.9005 (t) cc_final: 0.8594 (p) REVERT: W 99 GLU cc_start: 0.8797 (tt0) cc_final: 0.8336 (tt0) REVERT: 0 148 MET cc_start: 0.4726 (ttt) cc_final: 0.4516 (ttp) outliers start: 19 outliers final: 18 residues processed: 181 average time/residue: 0.2270 time to fit residues: 57.7338 Evaluate side-chains 180 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU 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 Q residue 102 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 44 SER 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 0 residue 166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 106 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103765 restraints weight = 39636.236| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.59 r_work: 0.3180 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10211 Z= 0.177 Angle : 0.546 8.541 13840 Z= 0.279 Chirality : 0.039 0.135 1648 Planarity : 0.004 0.054 1744 Dihedral : 3.946 15.587 1413 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.64 % Allowed : 18.28 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.24), residues: 1311 helix: 1.48 (0.18), residues: 861 sheet: -3.07 (0.48), residues: 87 loop : -1.54 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 66 TYR 0.010 0.002 TYR W 60 PHE 0.012 0.001 PHE G 223 TRP 0.002 0.001 TRP I 42 HIS 0.006 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00402 (10211) covalent geometry : angle 0.54615 (13840) hydrogen bonds : bond 0.04242 ( 648) hydrogen bonds : angle 4.04034 ( 1878) ********************** 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 179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.526 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 34 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8267 (tppp) REVERT: G 82 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7376 (ttp80) REVERT: H 87 GLN cc_start: 0.8021 (pt0) cc_final: 0.7754 (mt0) REVERT: P 66 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7435 (mtt-85) REVERT: P 70 MET cc_start: 0.8228 (mmp) cc_final: 0.7667 (mmt) REVERT: Q 66 ARG cc_start: 0.8118 (tpt90) cc_final: 0.7507 (tpt-90) REVERT: S 59 SER cc_start: 0.9158 (p) cc_final: 0.8915 (p) REVERT: S 85 SER cc_start: 0.8966 (t) cc_final: 0.8665 (m) REVERT: T 71 SER cc_start: 0.8851 (t) cc_final: 0.8504 (p) REVERT: W 69 ASN cc_start: 0.8227 (m-40) cc_final: 0.7905 (m-40) REVERT: W 71 SER cc_start: 0.8999 (t) cc_final: 0.8600 (p) REVERT: W 99 GLU cc_start: 0.8766 (tt0) cc_final: 0.8313 (tt0) outliers start: 17 outliers final: 16 residues processed: 172 average time/residue: 0.2436 time to fit residues: 58.5147 Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 35 ASN Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 97 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 35 ASN Chi-restraints excluded: chain W residue 82 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096308 restraints weight = 40239.205| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.66 r_work: 0.3061 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10211 Z= 0.193 Angle : 0.559 8.675 13840 Z= 0.286 Chirality : 0.039 0.135 1648 Planarity : 0.004 0.054 1744 Dihedral : 3.979 15.640 1413 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.74 % Allowed : 18.38 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1311 helix: 1.44 (0.18), residues: 861 sheet: -3.08 (0.47), residues: 87 loop : -1.58 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 66 TYR 0.011 0.002 TYR W 60 PHE 0.013 0.001 PHE G 223 TRP 0.003 0.001 TRP I 42 HIS 0.006 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00442 (10211) covalent geometry : angle 0.55926 (13840) hydrogen bonds : bond 0.04322 ( 648) hydrogen bonds : angle 4.06175 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4779.53 seconds wall clock time: 81 minutes 49.96 seconds (4909.96 seconds total)