Starting phenix.real_space_refine on Thu Mar 5 22:00:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9s_29877/03_2026/8g9s_29877.cif" } resolution = 3.4 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= 0.034 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 P 42 5.49 5 S 108 5.16 5 C 16056 2.51 5 N 4594 2.21 5 O 4958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 188 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25758 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2124 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Chain: "G" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1673 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "O" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 895 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 20, 'rna3p': 21} Chain: "K" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3223 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 2 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Time building chain proxies: 5.06, per 1000 atoms: 0.20 Number of scatterers: 25758 At special positions: 0 Unit cell: (120.054, 129.941, 206.21, 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 108 16.00 P 42 15.00 O 4958 8.00 N 4594 7.00 C 16056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 938.5 milliseconds 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5728 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 38 sheets defined 41.6% alpha, 15.2% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.955A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.530A pdb=" N LYS B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 106 removed outlier: 3.644A pdb=" N THR B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.714A pdb=" N GLN B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.799A pdb=" N HIS B 212 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 4.181A pdb=" N LEU B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.098A pdb=" N GLU B 274 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 275 " --> pdb=" O ASN B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'C' and resid 42 through 58 removed outlier: 3.843A pdb=" N LEU C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 186 through 193 removed outlier: 4.002A pdb=" N GLN C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 192 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.567A pdb=" N THR C 276 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.913A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.638A pdb=" N ALA D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.700A pdb=" N THR D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.668A pdb=" N VAL D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.737A pdb=" N LEU D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 58 removed outlier: 3.931A pdb=" N LEU E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 84 removed outlier: 3.725A pdb=" N LEU E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 90 through 106 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 115 through 119 removed outlier: 4.169A pdb=" N THR E 118 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 119 " --> pdb=" O MET E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 119' Processing helix chain 'E' and resid 185 through 193 removed outlier: 4.275A pdb=" N ALA E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 192 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 208 removed outlier: 3.846A pdb=" N VAL E 207 " --> pdb=" O TRP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 213 Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.728A pdb=" N LEU E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.750A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.571A pdb=" N ARG F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 195 through 208 Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'G' and resid 42 through 59 Processing helix chain 'G' and resid 73 through 82 removed outlier: 4.100A pdb=" N ALA G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 106 removed outlier: 3.923A pdb=" N GLU G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.952A pdb=" N ARG G 110 " --> pdb=" O TYR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 193 Processing helix chain 'G' and resid 195 through 213 removed outlier: 3.779A pdb=" N VAL G 207 " --> pdb=" O TRP G 203 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHE G 210 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP G 211 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP G 213 " --> pdb=" O MET G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 35 through 47 removed outlier: 4.567A pdb=" N GLY H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N SER H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 65 removed outlier: 3.505A pdb=" N ARG H 57 " --> pdb=" O GLY H 53 " (cutoff:3.500A) Proline residue: H 60 - end of helix Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.986A pdb=" N HIS H 85 " --> pdb=" O GLN H 81 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS H 86 " --> pdb=" O ILE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.612A pdb=" N GLN H 110 " --> pdb=" O TYR H 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE H 111 " --> pdb=" O HIS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 125 removed outlier: 3.504A pdb=" N ALA H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 35 through 47 removed outlier: 5.301A pdb=" N GLY I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 66 removed outlier: 4.770A pdb=" N VAL I 51 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.910A pdb=" N GLU I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 114 removed outlier: 3.537A pdb=" N ALA I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 47 removed outlier: 4.282A pdb=" N ARG J 39 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 66 removed outlier: 4.086A pdb=" N VAL J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 58 " --> pdb=" O THR J 54 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 94 through 114 removed outlier: 3.651A pdb=" N ALA J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 125 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.022A pdb=" N LEU M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 106 Processing helix chain 'M' and resid 106 through 112 Processing helix chain 'M' and resid 185 through 193 removed outlier: 3.610A pdb=" N ALA M 189 " --> pdb=" O SER M 185 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN M 191 " --> pdb=" O HIS M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 208 Processing helix chain 'M' and resid 239 through 246 removed outlier: 3.866A pdb=" N LEU M 243 " --> pdb=" O PRO M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'M' and resid 272 through 276 removed outlier: 3.656A pdb=" N THR M 276 " --> pdb=" O LEU M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 removed outlier: 3.635A pdb=" N ARG N 35 " --> pdb=" O PRO N 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN N 36 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 42 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 85 Processing helix chain 'N' and resid 117 through 132 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.572A pdb=" N SER K 16 " --> pdb=" O ARG K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 260 Processing helix chain 'K' and resid 281 through 290 removed outlier: 5.401A pdb=" N SER K 287 " --> pdb=" O GLU K 283 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET K 288 " --> pdb=" O SER K 284 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN K 290 " --> pdb=" O ALA K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 303 Processing helix chain 'K' and resid 304 through 312 removed outlier: 3.527A pdb=" N TYR K 308 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR K 312 " --> pdb=" O TYR K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 322 removed outlier: 3.908A pdb=" N LYS K 322 " --> pdb=" O PRO K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 362 Processing helix chain 'K' and resid 376 through 383 Processing helix chain 'K' and resid 393 through 408 removed outlier: 3.629A pdb=" N LEU K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN K 400 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 427 removed outlier: 3.885A pdb=" N LEU K 416 " --> pdb=" O PRO K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 448 Processing helix chain 'K' and resid 466 through 486 Processing helix chain 'K' and resid 492 through 504 removed outlier: 6.511A pdb=" N GLY K 499 " --> pdb=" O ASP K 495 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER K 500 " --> pdb=" O ARG K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 523 removed outlier: 3.837A pdb=" N VAL K 508 " --> pdb=" O THR K 504 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY K 510 " --> pdb=" O ILE K 506 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR K 511 " --> pdb=" O ALA K 507 " (cutoff:3.500A) Proline residue: K 517 - end of helix Processing helix chain 'K' and resid 525 through 541 Processing helix chain 'K' and resid 551 through 570 Processing helix chain 'K' and resid 573 through 582 removed outlier: 3.651A pdb=" N ALA K 582 " --> pdb=" O LEU K 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.784A pdb=" N ASN L 29 " --> pdb=" O GLN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 47 removed outlier: 6.531A pdb=" N GLY L 42 " --> pdb=" O ASP L 38 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 66 removed outlier: 4.051A pdb=" N VAL L 51 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY L 53 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR L 54 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Proline residue: L 60 - end of helix Processing helix chain 'L' and resid 70 through 85 removed outlier: 4.194A pdb=" N HIS L 85 " --> pdb=" O GLN L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 113 Processing helix chain 'L' and resid 116 through 125 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.542A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.604A pdb=" N SER B 134 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 131 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE B 183 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE B 133 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS B 181 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 7 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 14 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA B 223 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 148 removed outlier: 3.746A pdb=" N HIS B 145 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.629A pdb=" N ARG C 135 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.629A pdb=" N ARG C 135 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 7 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'C' and resid 247 through 250 Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.533A pdb=" N ASP D 14 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ALA D 223 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'D' and resid 247 through 251 Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.676A pdb=" N GLU E 38 " --> pdb=" O ASP E 33 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY E 39 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG E 135 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG E 179 " --> pdb=" O ARG E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 129 through 131 Processing sheet with id=AB8, first strand: chain 'E' and resid 247 through 251 Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.583A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.583A pdb=" N ARG F 135 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR F 7 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG F 6 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU F 230 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP F 8 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL F 228 " --> pdb=" O ASP F 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL F 10 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 226 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 12 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN F 220 " --> pdb=" O GLN F 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AC3, first strand: chain 'F' and resid 247 through 250 Processing sheet with id=AC4, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AC5, first strand: chain 'G' and resid 40 through 41 removed outlier: 6.535A pdb=" N ASP G 14 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA G 223 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLN G 16 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET G 221 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG G 224 " --> pdb=" O GLY G 284 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY G 284 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU G 226 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU G 282 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AC7, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'M' and resid 178 through 183 removed outlier: 6.929A pdb=" N ASP M 8 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL M 228 " --> pdb=" O ASP M 8 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL M 10 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU M 226 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU M 12 " --> pdb=" O ARG M 224 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN M 220 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL M 228 " --> pdb=" O ARG M 280 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 114 through 115 Processing sheet with id=AD1, first strand: chain 'M' and resid 143 through 145 Processing sheet with id=AD2, first strand: chain 'M' and resid 166 through 167 removed outlier: 3.583A pdb=" N MET M 167 " --> pdb=" O TYR A 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'M' and resid 248 through 251 Processing sheet with id=AD4, first strand: chain 'N' and resid 62 through 70 removed outlier: 6.786A pdb=" N ASP N 10 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA N 99 " --> pdb=" O SER N 8 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER N 8 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG N 101 " --> pdb=" O GLU N 6 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU N 6 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS N 103 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE N 4 " --> pdb=" O HIS N 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 62 through 70 removed outlier: 6.580A pdb=" N ARG N 101 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE N 54 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS N 103 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 170 through 172 Processing sheet with id=AD7, first strand: chain 'K' and resid 192 through 194 Processing sheet with id=AD8, first strand: chain 'K' and resid 210 through 211 Processing sheet with id=AD9, first strand: chain 'K' and resid 324 through 325 Processing sheet with id=AE1, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AE2, first strand: chain 'A' and resid 20 through 24 removed outlier: 3.532A pdb=" N ILE A 12 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 65 " --> pdb=" O ILE A 12 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6747 1.33 - 1.45: 5476 1.45 - 1.57: 13865 1.57 - 1.70: 83 1.70 - 1.82: 185 Bond restraints: 26356 Sorted by residual: bond pdb=" CA ASP C 213 " pdb=" CB ASP C 213 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.35e-02 5.49e+03 6.37e+00 bond pdb=" CG1 ILE M 147 " pdb=" CD1 ILE M 147 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.87e+00 bond pdb=" CA ASP C 8 " pdb=" CB ASP C 8 " ideal model delta sigma weight residual 1.534 1.496 0.037 1.72e-02 3.38e+03 4.74e+00 bond pdb=" CA GLY B 22 " pdb=" C GLY B 22 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.70e+00 bond pdb=" CB VAL C 50 " pdb=" CG2 VAL C 50 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 ... (remaining 26351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 33991 1.78 - 3.56: 1483 3.56 - 5.33: 214 5.33 - 7.11: 34 7.11 - 8.89: 9 Bond angle restraints: 35731 Sorted by residual: angle pdb=" C ARG B 224 " pdb=" N GLY B 225 " pdb=" CA GLY B 225 " ideal model delta sigma weight residual 122.33 119.18 3.15 7.30e-01 1.88e+00 1.86e+01 angle pdb=" N VAL G 258 " pdb=" CA VAL G 258 " pdb=" C VAL G 258 " ideal model delta sigma weight residual 106.21 109.99 -3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" C ASP M 157 " pdb=" N ALA M 158 " pdb=" CA ALA M 158 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CB ARG D 259 " pdb=" CG ARG D 259 " pdb=" CD ARG D 259 " ideal model delta sigma weight residual 111.30 119.09 -7.79 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA MET E 209 " pdb=" CB MET E 209 " pdb=" CG MET E 209 " ideal model delta sigma weight residual 114.10 107.56 6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 35726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15483 35.76 - 71.53: 345 71.53 - 107.29: 53 107.29 - 143.05: 3 143.05 - 178.81: 3 Dihedral angle restraints: 15887 sinusoidal: 6974 harmonic: 8913 Sorted by residual: dihedral pdb=" O4' C O 14 " pdb=" C1' C O 14 " pdb=" N1 C O 14 " pdb=" C2 C O 14 " ideal model delta sinusoidal sigma weight residual 200.00 42.17 157.83 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C O 38 " pdb=" C1' C O 38 " pdb=" N1 C O 38 " pdb=" C2 C O 38 " ideal model delta sinusoidal sigma weight residual 200.00 53.15 146.85 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C O 8 " pdb=" C1' C O 8 " pdb=" N1 C O 8 " pdb=" C2 C O 8 " ideal model delta sinusoidal sigma weight residual 200.00 66.11 133.89 1 1.50e+01 4.44e-03 7.22e+01 ... (remaining 15884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3195 0.063 - 0.125: 605 0.125 - 0.188: 62 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 3866 Sorted by residual: chirality pdb=" C3' U O 24 " pdb=" C4' U O 24 " pdb=" O3' U O 24 " pdb=" C2' U O 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB THR K 279 " pdb=" CA THR K 279 " pdb=" OG1 THR K 279 " pdb=" CG2 THR K 279 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' C O 31 " pdb=" O4' C O 31 " pdb=" C2' C O 31 " pdb=" N1 C O 31 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 3863 not shown) Planarity restraints: 4570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 77 " -0.021 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP L 77 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP L 77 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 77 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP L 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 47 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO H 48 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 127 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO D 128 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.033 5.00e-02 4.00e+02 ... (remaining 4567 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 540 2.61 - 3.18: 25668 3.18 - 3.75: 40805 3.75 - 4.33: 55110 4.33 - 4.90: 86984 Nonbonded interactions: 209107 Sorted by model distance: nonbonded pdb=" OG SER M 195 " pdb=" OD1 ASN M 197 " model vdw 2.037 3.040 nonbonded pdb=" OD2 ASP B 237 " pdb=" OG1 THR B 276 " model vdw 2.086 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" OP1 U O 13 " model vdw 2.086 3.120 nonbonded pdb=" NH2 ARG E 51 " pdb=" OP1 C O 31 " model vdw 2.094 3.120 nonbonded pdb=" OD2 ASP M 237 " pdb=" OG1 THR M 276 " model vdw 2.097 3.040 ... (remaining 209102 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 'B' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'G' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'M' and (resid 2 through 148 or resid 167 through 284)) } ncs_group { reference = (chain 'H' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'I' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'J' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = chain 'L' } 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: 1.110 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 24.620 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.008 0.086 26356 Z= 0.351 Angle : 0.851 8.889 35731 Z= 0.488 Chirality : 0.048 0.314 3866 Planarity : 0.005 0.061 4570 Dihedral : 16.325 178.815 10159 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.52 % Favored : 91.44 % Rotamer: Outliers : 0.04 % Allowed : 0.57 % Favored : 99.40 % 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 are not related in a simple way. whole: -1.55 (0.15), residues: 3062 helix: 0.42 (0.15), residues: 1116 sheet: -1.13 (0.21), residues: 585 loop : -2.25 (0.15), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 280 TYR 0.027 0.003 TYR H 12 PHE 0.030 0.003 PHE M 11 TRP 0.058 0.003 TRP L 77 HIS 0.020 0.002 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00760 (26356) covalent geometry : angle 0.85101 (35731) hydrogen bonds : bond 0.17097 ( 1028) hydrogen bonds : angle 7.56728 ( 3009) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.979 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: symmetry clash REVERT: C 103 CYS cc_start: 0.8560 (m) cc_final: 0.8201 (m) REVERT: C 272 ASN cc_start: 0.8958 (m110) cc_final: 0.8673 (m-40) REVERT: D 150 MET cc_start: 0.8868 (tpt) cc_final: 0.8487 (tpp) REVERT: E 111 THR cc_start: 0.8628 (m) cc_final: 0.8428 (p) REVERT: E 167 MET cc_start: 0.7910 (mmp) cc_final: 0.7501 (mmm) REVERT: F 116 MET cc_start: 0.9324 (mpp) cc_final: 0.8326 (mpp) REVERT: G 116 MET cc_start: 0.9063 (mpp) cc_final: 0.8420 (mpp) REVERT: H 116 ASP cc_start: 0.9299 (p0) cc_final: 0.8953 (t0) REVERT: I 25 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8972 (tm-30) REVERT: I 41 PHE cc_start: 0.9192 (t80) cc_final: 0.8856 (t80) REVERT: I 68 PHE cc_start: 0.7757 (t80) cc_final: 0.7530 (t80) REVERT: I 88 ARG cc_start: 0.8786 (tmm-80) cc_final: 0.8550 (ttp80) REVERT: J 65 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8772 (tttm) REVERT: N 165 THR cc_start: 0.6275 (p) cc_final: 0.5982 (p) REVERT: K 300 HIS cc_start: 0.8694 (m90) cc_final: 0.8149 (m-70) REVERT: K 327 LEU cc_start: 0.9340 (mm) cc_final: 0.8904 (pp) REVERT: L 9 ASP cc_start: 0.8702 (m-30) cc_final: 0.8480 (m-30) REVERT: L 56 MET cc_start: 0.8742 (mmp) cc_final: 0.8206 (ttt) REVERT: A 11 LYS cc_start: 0.8666 (tptt) cc_final: 0.8430 (tppt) REVERT: A 12 ILE cc_start: 0.8814 (tt) cc_final: 0.8456 (tt) REVERT: A 22 LYS cc_start: 0.8891 (mppt) cc_final: 0.8667 (mmmt) REVERT: A 28 GLU cc_start: 0.8426 (mp0) cc_final: 0.8225 (mp0) REVERT: A 67 LYS cc_start: 0.9501 (pptt) cc_final: 0.9137 (pptt) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1782 time to fit residues: 73.0921 Evaluate side-chains 214 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0050 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 85 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN F 74 ASN F 234 ASN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 GLN H 85 HIS M 124 GLN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 ASN L 61 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.085248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060110 restraints weight = 99077.908| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.68 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26356 Z= 0.135 Angle : 0.626 7.665 35731 Z= 0.336 Chirality : 0.043 0.236 3866 Planarity : 0.005 0.095 4570 Dihedral : 13.703 167.031 4057 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.83 % Allowed : 7.13 % Favored : 92.04 % 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 are not related in a simple way. whole: -0.77 (0.15), residues: 3062 helix: 1.04 (0.15), residues: 1174 sheet: -0.52 (0.23), residues: 516 loop : -1.95 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 278 TYR 0.016 0.002 TYR K 250 PHE 0.026 0.001 PHE H 111 TRP 0.027 0.002 TRP L 77 HIS 0.006 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00288 (26356) covalent geometry : angle 0.62582 (35731) hydrogen bonds : bond 0.04604 ( 1028) hydrogen bonds : angle 5.35480 ( 3009) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 278 time to evaluate : 1.091 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: B 209 MET cc_start: 0.8465 (tmm) cc_final: 0.7042 (tmm) REVERT: C 103 CYS cc_start: 0.8721 (m) cc_final: 0.8368 (m) REVERT: C 167 MET cc_start: 0.8765 (mmm) cc_final: 0.8444 (mmp) REVERT: C 209 MET cc_start: 0.8667 (tpp) cc_final: 0.8365 (tpp) REVERT: C 272 ASN cc_start: 0.9418 (m110) cc_final: 0.9216 (m110) REVERT: D 111 THR cc_start: 0.8922 (m) cc_final: 0.8557 (p) REVERT: D 150 MET cc_start: 0.8629 (tpt) cc_final: 0.8369 (tpp) REVERT: E 209 MET cc_start: 0.6794 (ttm) cc_final: 0.6288 (tpt) REVERT: F 116 MET cc_start: 0.9434 (mpp) cc_final: 0.8591 (mpp) REVERT: F 141 MET cc_start: 0.8380 (mpp) cc_final: 0.8164 (mpp) REVERT: F 167 MET cc_start: -0.1555 (ttt) cc_final: -0.2142 (ttp) REVERT: F 169 ARG cc_start: 0.8247 (mmt-90) cc_final: 0.8046 (mmp80) REVERT: F 178 TYR cc_start: 0.8888 (m-80) cc_final: 0.8673 (m-80) REVERT: F 209 MET cc_start: 0.8114 (ttp) cc_final: 0.7896 (tmm) REVERT: G 116 MET cc_start: 0.9026 (mpp) cc_final: 0.8429 (mpp) REVERT: H 77 TRP cc_start: 0.8426 (t60) cc_final: 0.7958 (t60) REVERT: H 87 GLN cc_start: 0.7931 (pp30) cc_final: 0.7728 (pp30) REVERT: H 89 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6735 (t80) REVERT: H 116 ASP cc_start: 0.9302 (p0) cc_final: 0.8952 (t0) REVERT: I 41 PHE cc_start: 0.9089 (t80) cc_final: 0.8884 (t80) REVERT: I 55 LEU cc_start: 0.9504 (mt) cc_final: 0.9252 (mt) REVERT: I 68 PHE cc_start: 0.7954 (t80) cc_final: 0.7484 (t80) REVERT: I 88 ARG cc_start: 0.8872 (tmm-80) cc_final: 0.8514 (ttp80) REVERT: I 106 TYR cc_start: 0.9195 (m-80) cc_final: 0.8952 (m-80) REVERT: J 22 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9000 (tm-30) REVERT: J 27 GLU cc_start: 0.8501 (mp0) cc_final: 0.8233 (mp0) REVERT: J 106 TYR cc_start: 0.9297 (m-80) cc_final: 0.9069 (m-80) REVERT: N 171 MET cc_start: 0.8970 (tpp) cc_final: 0.8719 (tpt) REVERT: K 300 HIS cc_start: 0.8585 (m90) cc_final: 0.7826 (m-70) REVERT: K 327 LEU cc_start: 0.9334 (mm) cc_final: 0.8779 (pp) REVERT: L 9 ASP cc_start: 0.8720 (m-30) cc_final: 0.8475 (m-30) REVERT: L 18 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8609 (t80) REVERT: L 40 TYR cc_start: 0.9156 (m-80) cc_final: 0.8953 (m-80) REVERT: L 56 MET cc_start: 0.8752 (mmp) cc_final: 0.7931 (ttt) outliers start: 22 outliers final: 10 residues processed: 288 average time/residue: 0.1711 time to fit residues: 78.2160 Evaluate side-chains 233 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 195 CYS Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 2 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 240 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.082846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.057755 restraints weight = 102232.397| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.61 r_work: 0.2920 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26356 Z= 0.224 Angle : 0.658 8.487 35731 Z= 0.353 Chirality : 0.044 0.280 3866 Planarity : 0.005 0.099 4570 Dihedral : 13.680 168.458 4057 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.32 % Allowed : 11.58 % Favored : 87.10 % 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 are not related in a simple way. whole: -0.73 (0.15), residues: 3062 helix: 1.10 (0.16), residues: 1176 sheet: -0.44 (0.23), residues: 516 loop : -1.97 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 51 TYR 0.027 0.002 TYR N 139 PHE 0.028 0.002 PHE H 111 TRP 0.008 0.001 TRP C 203 HIS 0.007 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00495 (26356) covalent geometry : angle 0.65821 (35731) hydrogen bonds : bond 0.04908 ( 1028) hydrogen bonds : angle 5.38333 ( 3009) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.043 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: B 209 MET cc_start: 0.8714 (tmm) cc_final: 0.7080 (tmm) REVERT: C 103 CYS cc_start: 0.9309 (m) cc_final: 0.9048 (m) REVERT: C 167 MET cc_start: 0.8979 (mmm) cc_final: 0.8381 (mmm) REVERT: C 209 MET cc_start: 0.8634 (tpp) cc_final: 0.8270 (tpp) REVERT: C 255 VAL cc_start: 0.8887 (m) cc_final: 0.8664 (p) REVERT: D 25 ASP cc_start: 0.8534 (m-30) cc_final: 0.8318 (m-30) REVERT: D 150 MET cc_start: 0.9169 (tpt) cc_final: 0.8838 (tpp) REVERT: E 167 MET cc_start: 0.7956 (mmm) cc_final: 0.7735 (mmm) REVERT: F 116 MET cc_start: 0.9431 (mpp) cc_final: 0.8325 (mpp) REVERT: F 141 MET cc_start: 0.8460 (mpp) cc_final: 0.8220 (mpp) REVERT: F 209 MET cc_start: 0.8278 (ttp) cc_final: 0.7960 (tmm) REVERT: G 116 MET cc_start: 0.8849 (mpp) cc_final: 0.8649 (mpp) REVERT: G 178 TYR cc_start: 0.8641 (m-80) cc_final: 0.8291 (m-80) REVERT: H 87 GLN cc_start: 0.8081 (pp30) cc_final: 0.7814 (pp30) REVERT: H 89 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7131 (t80) REVERT: H 116 ASP cc_start: 0.9269 (p0) cc_final: 0.8941 (t0) REVERT: H 122 PHE cc_start: 0.8645 (t80) cc_final: 0.8365 (t80) REVERT: I 39 ARG cc_start: 0.8904 (mtp180) cc_final: 0.8485 (ttm170) REVERT: I 40 TYR cc_start: 0.8675 (m-10) cc_final: 0.8289 (m-10) REVERT: I 41 PHE cc_start: 0.9215 (t80) cc_final: 0.8924 (t80) REVERT: I 55 LEU cc_start: 0.9519 (mt) cc_final: 0.9298 (mt) REVERT: I 68 PHE cc_start: 0.8051 (t80) cc_final: 0.7528 (t80) REVERT: I 88 ARG cc_start: 0.8832 (tmm-80) cc_final: 0.8475 (ttp80) REVERT: J 57 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8926 (mtp85) REVERT: J 68 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: N 171 MET cc_start: 0.8965 (tpp) cc_final: 0.8755 (tpt) REVERT: K 300 HIS cc_start: 0.8707 (m90) cc_final: 0.7949 (m-70) REVERT: K 327 LEU cc_start: 0.9392 (mm) cc_final: 0.8786 (pp) REVERT: L 9 ASP cc_start: 0.8561 (m-30) cc_final: 0.8336 (m-30) outliers start: 35 outliers final: 17 residues processed: 255 average time/residue: 0.1736 time to fit residues: 69.5771 Evaluate side-chains 237 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 75 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 40 optimal weight: 0.3980 chunk 168 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 176 optimal weight: 5.9990 overall best weight: 1.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 272 ASN F 16 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN I 8 GLN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 HIS K 518 HIS ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.084722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059690 restraints weight = 99898.080| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.66 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26356 Z= 0.122 Angle : 0.569 8.361 35731 Z= 0.302 Chirality : 0.041 0.224 3866 Planarity : 0.004 0.081 4570 Dihedral : 13.509 164.762 4057 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.70 % Allowed : 13.80 % Favored : 84.50 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 3062 helix: 1.32 (0.16), residues: 1183 sheet: -0.40 (0.23), residues: 521 loop : -1.78 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.018 0.001 TYR N 139 PHE 0.027 0.001 PHE H 111 TRP 0.008 0.001 TRP K 357 HIS 0.006 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00263 (26356) covalent geometry : angle 0.56943 (35731) hydrogen bonds : bond 0.03874 ( 1028) hydrogen bonds : angle 4.80637 ( 3009) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.978 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: B 209 MET cc_start: 0.8343 (tmm) cc_final: 0.7612 (tmm) REVERT: C 102 MET cc_start: 0.8492 (mmt) cc_final: 0.8272 (mmm) REVERT: C 103 CYS cc_start: 0.8734 (m) cc_final: 0.8365 (m) REVERT: C 142 THR cc_start: 0.9322 (p) cc_final: 0.9072 (t) REVERT: C 167 MET cc_start: 0.8830 (mmm) cc_final: 0.8443 (mmm) REVERT: C 209 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8023 (tpp) REVERT: D 77 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8988 (tt) REVERT: E 102 MET cc_start: 0.9347 (mmt) cc_final: 0.8965 (mmm) REVERT: E 167 MET cc_start: 0.7405 (mmm) cc_final: 0.7108 (mmm) REVERT: F 116 MET cc_start: 0.9492 (mpp) cc_final: 0.8679 (mpp) REVERT: F 141 MET cc_start: 0.8550 (mpp) cc_final: 0.8236 (mpp) REVERT: F 209 MET cc_start: 0.8083 (ttp) cc_final: 0.7794 (tmm) REVERT: G 116 MET cc_start: 0.9145 (mpp) cc_final: 0.8725 (mpp) REVERT: G 178 TYR cc_start: 0.8684 (m-80) cc_final: 0.8261 (m-80) REVERT: G 209 MET cc_start: 0.4177 (OUTLIER) cc_final: 0.3949 (ttt) REVERT: G 221 MET cc_start: 0.5386 (ptt) cc_final: 0.5097 (ptt) REVERT: H 87 GLN cc_start: 0.8461 (pp30) cc_final: 0.8254 (pp30) REVERT: H 89 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7100 (t80) REVERT: H 116 ASP cc_start: 0.9347 (p0) cc_final: 0.8942 (t0) REVERT: I 39 ARG cc_start: 0.9041 (mtp180) cc_final: 0.8715 (ttp-170) REVERT: I 41 PHE cc_start: 0.9221 (t80) cc_final: 0.8905 (t80) REVERT: I 55 LEU cc_start: 0.9517 (mt) cc_final: 0.9268 (mt) REVERT: I 88 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8529 (ttp80) REVERT: J 22 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9045 (tm-30) REVERT: J 68 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: K 300 HIS cc_start: 0.8521 (m90) cc_final: 0.7750 (m-70) REVERT: K 325 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7719 (t80) REVERT: K 327 LEU cc_start: 0.9269 (mm) cc_final: 0.8872 (pp) REVERT: L 9 ASP cc_start: 0.8659 (m-30) cc_final: 0.8417 (m-30) REVERT: L 56 MET cc_start: 0.8501 (mmp) cc_final: 0.7480 (ttt) REVERT: A 47 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8865 (tp30) outliers start: 45 outliers final: 24 residues processed: 278 average time/residue: 0.1684 time to fit residues: 74.2055 Evaluate side-chains 250 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 115 optimal weight: 0.0370 chunk 134 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN M 130 GLN K 313 ASN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.078774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054096 restraints weight = 107708.778| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.67 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 26356 Z= 0.303 Angle : 0.715 8.024 35731 Z= 0.381 Chirality : 0.045 0.309 3866 Planarity : 0.005 0.045 4570 Dihedral : 13.643 169.919 4057 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.64 % Allowed : 15.42 % Favored : 81.94 % 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 are not related in a simple way. whole: -0.74 (0.15), residues: 3062 helix: 1.12 (0.16), residues: 1179 sheet: -0.77 (0.22), residues: 570 loop : -1.89 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 80 TYR 0.032 0.002 TYR N 139 PHE 0.030 0.002 PHE H 111 TRP 0.016 0.002 TRP C 203 HIS 0.008 0.001 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00667 (26356) covalent geometry : angle 0.71458 (35731) hydrogen bonds : bond 0.05035 ( 1028) hydrogen bonds : angle 5.35666 ( 3009) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 1.049 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: C 103 CYS cc_start: 0.8676 (m) cc_final: 0.8280 (m) REVERT: C 209 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8095 (tpp) REVERT: E 167 MET cc_start: 0.7610 (mmm) cc_final: 0.7311 (mmm) REVERT: E 209 MET cc_start: 0.7555 (tpp) cc_final: 0.7289 (tpp) REVERT: F 116 MET cc_start: 0.9394 (mpp) cc_final: 0.8486 (mpp) REVERT: F 141 MET cc_start: 0.8457 (mpp) cc_final: 0.8254 (mpp) REVERT: F 209 MET cc_start: 0.8260 (ttp) cc_final: 0.7764 (tmm) REVERT: G 116 MET cc_start: 0.8928 (mpp) cc_final: 0.8282 (mpp) REVERT: G 178 TYR cc_start: 0.8802 (m-80) cc_final: 0.8489 (m-80) REVERT: G 209 MET cc_start: 0.4596 (OUTLIER) cc_final: 0.4343 (ttt) REVERT: G 221 MET cc_start: 0.5483 (ptt) cc_final: 0.5115 (ptt) REVERT: H 89 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7113 (t80) REVERT: H 124 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: I 39 ARG cc_start: 0.9028 (mtp180) cc_final: 0.8724 (ttm170) REVERT: I 40 TYR cc_start: 0.8784 (m-10) cc_final: 0.8528 (m-10) REVERT: I 88 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8446 (tmm-80) REVERT: J 57 ARG cc_start: 0.9147 (mtp85) cc_final: 0.8246 (mtt-85) REVERT: J 68 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: M 31 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6958 (mtt-85) REVERT: N 81 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8561 (mm) REVERT: K 11 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.9068 (mt0) REVERT: K 300 HIS cc_start: 0.8503 (m90) cc_final: 0.8113 (m-70) REVERT: L 40 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8923 (m-80) REVERT: L 56 MET cc_start: 0.8497 (mmp) cc_final: 0.8103 (ttt) outliers start: 70 outliers final: 41 residues processed: 270 average time/residue: 0.1647 time to fit residues: 70.6439 Evaluate side-chains 266 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 40 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 35 GLN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.079153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054528 restraints weight = 107595.788| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.65 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26356 Z= 0.255 Angle : 0.670 13.425 35731 Z= 0.356 Chirality : 0.044 0.299 3866 Planarity : 0.004 0.045 4570 Dihedral : 13.624 169.694 4057 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.94 % Allowed : 15.80 % Favored : 81.26 % 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 are not related in a simple way. whole: -0.76 (0.15), residues: 3062 helix: 1.14 (0.16), residues: 1178 sheet: -0.70 (0.22), residues: 532 loop : -1.96 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 51 TYR 0.029 0.002 TYR N 139 PHE 0.030 0.002 PHE H 111 TRP 0.011 0.001 TRP C 203 HIS 0.007 0.001 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00563 (26356) covalent geometry : angle 0.67016 (35731) hydrogen bonds : bond 0.04655 ( 1028) hydrogen bonds : angle 5.21026 ( 3009) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 220 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8333 (tt) REVERT: C 90 GLU cc_start: 0.9595 (tm-30) cc_final: 0.9362 (tm-30) REVERT: C 103 CYS cc_start: 0.8663 (m) cc_final: 0.8315 (m) REVERT: C 167 MET cc_start: 0.9001 (mmm) cc_final: 0.8578 (mmm) REVERT: C 209 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8051 (tpp) REVERT: E 167 MET cc_start: 0.7574 (mmm) cc_final: 0.7288 (mmm) REVERT: F 116 MET cc_start: 0.9410 (mpp) cc_final: 0.8508 (mpp) REVERT: F 141 MET cc_start: 0.8431 (mpp) cc_final: 0.8214 (mpp) REVERT: F 209 MET cc_start: 0.8282 (ttp) cc_final: 0.7763 (tmm) REVERT: G 116 MET cc_start: 0.8935 (mpp) cc_final: 0.8305 (mpp) REVERT: G 178 TYR cc_start: 0.8815 (m-80) cc_final: 0.8469 (m-80) REVERT: G 221 MET cc_start: 0.5747 (ptt) cc_final: 0.5522 (ptt) REVERT: H 89 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7098 (t80) REVERT: H 124 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: I 38 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8133 (t0) REVERT: I 39 ARG cc_start: 0.9015 (mtp180) cc_final: 0.8765 (mtp180) REVERT: I 41 PHE cc_start: 0.9187 (t80) cc_final: 0.8863 (t80) REVERT: I 88 ARG cc_start: 0.8794 (tmm-80) cc_final: 0.8404 (ttp80) REVERT: J 68 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: M 31 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6899 (mtt-85) REVERT: N 81 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8585 (mm) REVERT: K 11 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9028 (mt0) REVERT: K 288 MET cc_start: 0.9188 (mmp) cc_final: 0.8957 (tpp) REVERT: K 300 HIS cc_start: 0.8532 (m90) cc_final: 0.7939 (m-70) REVERT: K 325 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7732 (t80) REVERT: L 40 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8933 (m-80) outliers start: 78 outliers final: 54 residues processed: 280 average time/residue: 0.1690 time to fit residues: 75.0941 Evaluate side-chains 277 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 212 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 393 LEU Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 263 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 ASN K 518 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.080734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055882 restraints weight = 105881.726| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 4.69 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26356 Z= 0.153 Angle : 0.602 11.624 35731 Z= 0.317 Chirality : 0.042 0.247 3866 Planarity : 0.004 0.080 4570 Dihedral : 13.478 166.225 4057 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.83 % Allowed : 17.08 % Favored : 80.09 % 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 are not related in a simple way. whole: -0.50 (0.15), residues: 3062 helix: 1.33 (0.16), residues: 1182 sheet: -0.38 (0.23), residues: 499 loop : -1.86 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.024 0.001 TYR N 139 PHE 0.028 0.001 PHE H 111 TRP 0.008 0.001 TRP N 43 HIS 0.006 0.001 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00339 (26356) covalent geometry : angle 0.60200 (35731) hydrogen bonds : bond 0.04029 ( 1028) hydrogen bonds : angle 4.85187 ( 3009) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 0.925 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: C 90 GLU cc_start: 0.9564 (tm-30) cc_final: 0.9312 (tm-30) REVERT: C 103 CYS cc_start: 0.8685 (m) cc_final: 0.8334 (m) REVERT: C 167 MET cc_start: 0.8965 (mmm) cc_final: 0.8534 (mmm) REVERT: C 209 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7945 (tpp) REVERT: D 150 MET cc_start: 0.8181 (ttt) cc_final: 0.7814 (ttp) REVERT: E 72 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7362 (pt) REVERT: E 102 MET cc_start: 0.9422 (mmt) cc_final: 0.9029 (mmm) REVERT: E 167 MET cc_start: 0.7261 (mmm) cc_final: 0.6981 (mmm) REVERT: E 209 MET cc_start: 0.7963 (tpp) cc_final: 0.7067 (tpp) REVERT: F 116 MET cc_start: 0.9480 (mpp) cc_final: 0.8670 (mpp) REVERT: F 141 MET cc_start: 0.8344 (mpp) cc_final: 0.8138 (mpp) REVERT: F 209 MET cc_start: 0.8238 (ttp) cc_final: 0.7856 (tmm) REVERT: G 116 MET cc_start: 0.9092 (mpp) cc_final: 0.8621 (mpp) REVERT: G 178 TYR cc_start: 0.8789 (m-80) cc_final: 0.8425 (m-80) REVERT: H 89 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7341 (t80) REVERT: I 38 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.7998 (t0) REVERT: I 39 ARG cc_start: 0.8969 (mtp180) cc_final: 0.8428 (ttp-170) REVERT: I 40 TYR cc_start: 0.8640 (m-10) cc_final: 0.8204 (m-10) REVERT: I 41 PHE cc_start: 0.9177 (t80) cc_final: 0.8904 (t80) REVERT: I 55 LEU cc_start: 0.9483 (mt) cc_final: 0.9262 (mt) REVERT: I 65 LYS cc_start: 0.9059 (pptt) cc_final: 0.8800 (pptt) REVERT: I 88 ARG cc_start: 0.8792 (tmm-80) cc_final: 0.8396 (ttp80) REVERT: J 68 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: M 31 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6821 (mtt-85) REVERT: M 102 MET cc_start: 0.7768 (ptp) cc_final: 0.7546 (ptm) REVERT: N 81 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8511 (mm) REVERT: N 195 CYS cc_start: 0.9461 (t) cc_final: 0.9201 (p) REVERT: K 11 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9057 (mt0) REVERT: K 300 HIS cc_start: 0.8482 (m90) cc_final: 0.8071 (m-70) REVERT: K 325 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7655 (t80) REVERT: L 40 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8917 (m-80) REVERT: L 56 MET cc_start: 0.8381 (mmp) cc_final: 0.7903 (ttt) outliers start: 75 outliers final: 47 residues processed: 286 average time/residue: 0.1630 time to fit residues: 74.5772 Evaluate side-chains 276 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 222 ASN Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 16 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS K 518 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.080688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055837 restraints weight = 106123.925| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.69 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26356 Z= 0.164 Angle : 0.614 9.955 35731 Z= 0.322 Chirality : 0.042 0.248 3866 Planarity : 0.004 0.065 4570 Dihedral : 13.418 165.965 4057 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.45 % Allowed : 17.91 % Favored : 79.64 % 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 are not related in a simple way. whole: -0.44 (0.15), residues: 3062 helix: 1.37 (0.16), residues: 1181 sheet: -0.45 (0.23), residues: 525 loop : -1.79 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 80 TYR 0.024 0.001 TYR N 139 PHE 0.031 0.001 PHE H 111 TRP 0.007 0.001 TRP K 357 HIS 0.006 0.001 HIS G 187 Details of bonding type rmsd covalent geometry : bond 0.00364 (26356) covalent geometry : angle 0.61432 (35731) hydrogen bonds : bond 0.04053 ( 1028) hydrogen bonds : angle 4.82598 ( 3009) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 GLU cc_start: 0.9538 (tm-30) cc_final: 0.9332 (tm-30) REVERT: C 103 CYS cc_start: 0.8694 (m) cc_final: 0.8342 (m) REVERT: C 167 MET cc_start: 0.9014 (mmm) cc_final: 0.8594 (mmm) REVERT: C 209 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8077 (tpp) REVERT: D 17 ASP cc_start: 0.8568 (m-30) cc_final: 0.8313 (m-30) REVERT: D 150 MET cc_start: 0.8311 (ttt) cc_final: 0.8017 (ttt) REVERT: E 72 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7404 (pt) REVERT: E 102 MET cc_start: 0.9283 (mmt) cc_final: 0.9003 (mmm) REVERT: E 167 MET cc_start: 0.7346 (mmm) cc_final: 0.7030 (mmm) REVERT: E 209 MET cc_start: 0.7944 (tpp) cc_final: 0.7358 (tpp) REVERT: F 116 MET cc_start: 0.9506 (mpp) cc_final: 0.8716 (mpp) REVERT: F 141 MET cc_start: 0.8347 (mpp) cc_final: 0.8131 (mpp) REVERT: F 209 MET cc_start: 0.8398 (ttp) cc_final: 0.7778 (tmm) REVERT: G 116 MET cc_start: 0.9052 (mpp) cc_final: 0.8548 (mpp) REVERT: G 178 TYR cc_start: 0.8796 (m-80) cc_final: 0.8439 (m-80) REVERT: H 89 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7357 (t80) REVERT: I 38 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8119 (t0) REVERT: I 39 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8739 (mtp180) REVERT: I 41 PHE cc_start: 0.9201 (t80) cc_final: 0.8910 (t80) REVERT: I 55 LEU cc_start: 0.9482 (mt) cc_final: 0.9235 (mt) REVERT: I 65 LYS cc_start: 0.9107 (pptt) cc_final: 0.8856 (pptt) REVERT: I 88 ARG cc_start: 0.8835 (tmm-80) cc_final: 0.8441 (ttp80) REVERT: J 27 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8819 (mm-30) REVERT: J 68 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: M 31 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6879 (mtt-85) REVERT: M 102 MET cc_start: 0.7782 (ptp) cc_final: 0.7575 (ptm) REVERT: N 81 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8548 (mm) REVERT: N 195 CYS cc_start: 0.9497 (t) cc_final: 0.9155 (p) REVERT: K 11 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9027 (mt0) REVERT: K 288 MET cc_start: 0.9129 (mmp) cc_final: 0.8902 (tpp) REVERT: K 300 HIS cc_start: 0.8446 (m90) cc_final: 0.7864 (m-70) REVERT: K 325 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7667 (t80) REVERT: L 40 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8913 (m-80) REVERT: L 56 MET cc_start: 0.8397 (mmp) cc_final: 0.7841 (ttt) outliers start: 65 outliers final: 47 residues processed: 277 average time/residue: 0.1660 time to fit residues: 73.7185 Evaluate side-chains 279 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 222 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 273 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.084020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058549 restraints weight = 101027.916| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.75 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26356 Z= 0.194 Angle : 0.636 10.251 35731 Z= 0.334 Chirality : 0.043 0.263 3866 Planarity : 0.004 0.043 4570 Dihedral : 13.427 166.694 4057 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.83 % Allowed : 17.68 % Favored : 79.49 % 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 are not related in a simple way. whole: -0.49 (0.15), residues: 3062 helix: 1.31 (0.16), residues: 1182 sheet: -0.47 (0.23), residues: 524 loop : -1.79 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 57 TYR 0.026 0.002 TYR N 139 PHE 0.031 0.002 PHE H 111 TRP 0.009 0.001 TRP C 203 HIS 0.005 0.001 HIS H 62 Details of bonding type rmsd covalent geometry : bond 0.00431 (26356) covalent geometry : angle 0.63644 (35731) hydrogen bonds : bond 0.04206 ( 1028) hydrogen bonds : angle 4.91627 ( 3009) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 1.015 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: C 103 CYS cc_start: 0.8658 (m) cc_final: 0.8274 (m) REVERT: C 167 MET cc_start: 0.8897 (mmm) cc_final: 0.8568 (mmm) REVERT: C 209 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8164 (tpp) REVERT: D 150 MET cc_start: 0.8399 (ttt) cc_final: 0.8073 (ttt) REVERT: D 276 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (p) REVERT: E 167 MET cc_start: 0.7333 (mmm) cc_final: 0.6958 (mmm) REVERT: E 209 MET cc_start: 0.7944 (tpp) cc_final: 0.7294 (tpp) REVERT: F 116 MET cc_start: 0.9461 (mpp) cc_final: 0.8612 (mpp) REVERT: F 178 TYR cc_start: 0.9010 (m-80) cc_final: 0.8564 (m-80) REVERT: G 116 MET cc_start: 0.9117 (mpp) cc_final: 0.8634 (mpp) REVERT: G 178 TYR cc_start: 0.8791 (m-80) cc_final: 0.8439 (m-80) REVERT: H 89 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7342 (t80) REVERT: I 38 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8079 (t0) REVERT: I 39 ARG cc_start: 0.8999 (mtp180) cc_final: 0.8698 (mtp180) REVERT: I 40 TYR cc_start: 0.8697 (m-10) cc_final: 0.8432 (m-10) REVERT: I 41 PHE cc_start: 0.9226 (t80) cc_final: 0.8909 (t80) REVERT: I 55 LEU cc_start: 0.9514 (mt) cc_final: 0.9250 (mt) REVERT: I 65 LYS cc_start: 0.9176 (pptt) cc_final: 0.8932 (pptt) REVERT: I 88 ARG cc_start: 0.8852 (tmm-80) cc_final: 0.8473 (ttp80) REVERT: J 27 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8791 (mm-30) REVERT: J 68 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: M 31 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6986 (mtt-85) REVERT: N 81 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8514 (mm) REVERT: N 195 CYS cc_start: 0.9527 (t) cc_final: 0.9217 (p) REVERT: K 11 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.9046 (mt0) REVERT: K 300 HIS cc_start: 0.8484 (m90) cc_final: 0.7873 (m-70) REVERT: K 325 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7648 (t80) REVERT: L 40 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: L 56 MET cc_start: 0.8610 (mmp) cc_final: 0.7531 (ttt) outliers start: 75 outliers final: 57 residues processed: 282 average time/residue: 0.1660 time to fit residues: 74.4562 Evaluate side-chains 290 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 167 MET Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 201 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 303 optimal weight: 5.9990 chunk 290 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.082218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057330 restraints weight = 104704.495| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.76 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26356 Z= 0.122 Angle : 0.616 11.644 35731 Z= 0.317 Chirality : 0.042 0.216 3866 Planarity : 0.004 0.086 4570 Dihedral : 13.311 163.748 4057 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.11 % Allowed : 18.36 % Favored : 79.52 % 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 are not related in a simple way. whole: -0.33 (0.15), residues: 3062 helix: 1.43 (0.16), residues: 1183 sheet: -0.26 (0.23), residues: 520 loop : -1.74 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 224 TYR 0.017 0.001 TYR N 139 PHE 0.030 0.001 PHE H 111 TRP 0.013 0.001 TRP D 203 HIS 0.005 0.001 HIS F 187 Details of bonding type rmsd covalent geometry : bond 0.00271 (26356) covalent geometry : angle 0.61554 (35731) hydrogen bonds : bond 0.03590 ( 1028) hydrogen bonds : angle 4.59957 ( 3009) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6124 Ramachandran restraints generated. 3062 Oldfield, 0 Emsley, 3062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.714 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: symmetry clash REVERT: C 81 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.8033 (t-90) REVERT: C 103 CYS cc_start: 0.8712 (m) cc_final: 0.8288 (m) REVERT: C 167 MET cc_start: 0.8927 (mmm) cc_final: 0.8517 (mmm) REVERT: D 17 ASP cc_start: 0.8508 (m-30) cc_final: 0.8252 (m-30) REVERT: D 35 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8451 (tm-30) REVERT: D 276 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (p) REVERT: E 167 MET cc_start: 0.7042 (mmm) cc_final: 0.6750 (mmm) REVERT: E 209 MET cc_start: 0.7938 (tpp) cc_final: 0.7206 (tpp) REVERT: F 116 MET cc_start: 0.9514 (mpp) cc_final: 0.8760 (mpp) REVERT: F 141 MET cc_start: 0.8344 (mpp) cc_final: 0.8122 (mpp) REVERT: F 178 TYR cc_start: 0.8966 (m-80) cc_final: 0.8460 (m-80) REVERT: F 209 MET cc_start: 0.8378 (tmm) cc_final: 0.8035 (ttp) REVERT: G 116 MET cc_start: 0.9180 (mpp) cc_final: 0.8761 (mpp) REVERT: G 178 TYR cc_start: 0.8770 (m-80) cc_final: 0.8397 (m-80) REVERT: G 264 TYR cc_start: 0.7642 (m-80) cc_final: 0.7403 (m-80) REVERT: H 71 ARG cc_start: 0.8564 (mmp80) cc_final: 0.8355 (mmm160) REVERT: H 89 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7676 (t80) REVERT: I 38 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8098 (t70) REVERT: I 39 ARG cc_start: 0.8935 (mtp180) cc_final: 0.8649 (mtp180) REVERT: I 40 TYR cc_start: 0.8638 (m-10) cc_final: 0.8379 (m-10) REVERT: I 41 PHE cc_start: 0.9153 (t80) cc_final: 0.8811 (t80) REVERT: I 52 PHE cc_start: 0.9025 (m-80) cc_final: 0.8287 (m-80) REVERT: I 65 LYS cc_start: 0.9088 (pptt) cc_final: 0.8841 (pptt) REVERT: I 88 ARG cc_start: 0.8815 (tmm-80) cc_final: 0.8436 (ttp80) REVERT: J 27 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8757 (mm-30) REVERT: J 41 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: J 57 ARG cc_start: 0.9131 (mtp85) cc_final: 0.8205 (mtt-85) REVERT: J 68 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: M 31 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6864 (mtt-85) REVERT: M 116 MET cc_start: 0.7295 (tpp) cc_final: 0.7001 (mmm) REVERT: N 81 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8469 (mm) REVERT: N 165 THR cc_start: 0.7170 (p) cc_final: 0.6600 (p) REVERT: N 166 GLN cc_start: 0.8444 (pm20) cc_final: 0.8239 (pm20) REVERT: N 195 CYS cc_start: 0.9464 (t) cc_final: 0.9112 (p) REVERT: K 11 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.9057 (mt0) REVERT: K 288 MET cc_start: 0.8988 (tpp) cc_final: 0.8770 (tpp) REVERT: K 300 HIS cc_start: 0.8387 (m90) cc_final: 0.7749 (m-70) REVERT: K 325 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7567 (t80) REVERT: L 40 TYR cc_start: 0.9231 (m-80) cc_final: 0.8953 (m-80) REVERT: L 56 MET cc_start: 0.8471 (mmp) cc_final: 0.7935 (ttt) outliers start: 56 outliers final: 39 residues processed: 281 average time/residue: 0.1711 time to fit residues: 76.2968 Evaluate side-chains 277 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 41 PHE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 477 VAL Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 38 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 275 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 185 optimal weight: 5.9990 chunk 86 optimal weight: 0.0170 chunk 179 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS K 518 HIS ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.081756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056951 restraints weight = 104989.963| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.72 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26356 Z= 0.138 Angle : 0.609 12.184 35731 Z= 0.315 Chirality : 0.042 0.226 3866 Planarity : 0.004 0.079 4570 Dihedral : 13.271 164.548 4057 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.15 % Allowed : 18.33 % Favored : 79.52 % 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 are not related in a simple way. whole: -0.28 (0.15), residues: 3062 helix: 1.44 (0.16), residues: 1183 sheet: -0.11 (0.23), residues: 515 loop : -1.73 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 224 TYR 0.021 0.001 TYR N 139 PHE 0.021 0.001 PHE L 41 TRP 0.008 0.001 TRP K 357 HIS 0.005 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00307 (26356) covalent geometry : angle 0.60904 (35731) hydrogen bonds : bond 0.03689 ( 1028) hydrogen bonds : angle 4.60052 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.86 seconds wall clock time: 107 minutes 9.57 seconds (6429.57 seconds total)