Starting phenix.real_space_refine on Sun Jul 5 04:55:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9s_29877/07_2026/8g9s_29877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9s_29877/07_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_29877/07_2026/8g9s_29877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9s_29877/07_2026/8g9s_29877.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9s_29877/07_2026/8g9s_29877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9s_29877/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.98, per 1000 atoms: 0.23 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: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.70 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: 5.18 Time building geometry restraints manager: 2.81 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=" N9 A O 7 " pdb=" C4 A O 7 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.25e+01 bond pdb=" N1 C O 31 " pdb=" C6 C O 31 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.03e+01 bond pdb=" N3 C O 14 " pdb=" C4 C O 14 " ideal model delta sigma weight residual 1.335 1.314 0.021 7.00e-03 2.04e+04 9.38e+00 bond pdb=" N3 A O 5 " pdb=" C4 A O 5 " ideal model delta sigma weight residual 1.344 1.326 0.018 6.00e-03 2.78e+04 9.13e+00 bond pdb=" N7 A O 15 " pdb=" C5 A O 15 " ideal model delta sigma weight residual 1.388 1.371 0.017 6.00e-03 2.78e+04 8.36e+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=" C1' C O 17 " pdb=" N1 C O 17 " pdb=" C2 C O 17 " ideal model delta sigma weight residual 118.80 124.18 -5.38 1.10e+00 8.26e-01 2.39e+01 angle pdb=" C1' C O 8 " pdb=" N1 C O 8 " pdb=" C2 C O 8 " ideal model delta sigma weight residual 118.80 124.13 -5.33 1.10e+00 8.26e-01 2.35e+01 angle pdb=" N1 C O 8 " pdb=" C2 C O 8 " pdb=" O2 C O 8 " ideal model delta sigma weight residual 118.90 121.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O2 C O 14 " pdb=" C2 C O 14 " pdb=" N3 C O 14 " ideal model delta sigma weight residual 121.90 118.64 3.26 7.00e-01 2.04e+00 2.17e+01 angle pdb=" N1 C O 14 " pdb=" C2 C O 14 " pdb=" O2 C O 14 " ideal model delta sigma weight residual 118.90 121.52 -2.62 6.00e-01 2.78e+00 1.91e+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: 1.640 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.580 Find NCS groups from input model: 0.500 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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= 0.385 Angle : 0.851 8.889 35731 Z= 0.516 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/Z covalent geometry : bond 0.00760 / 0.39 (26356) covalent geometry : angle 0.85100 / 0.52 (35731) hydrogen bonds : bond 0.17097 / 11.34 ( 1028) hydrogen bonds : angle 7.56728 / 5.38 ( 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 : 0.804 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: 0.1783 time to fit residues: 73.6659 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 : 0.938 ------------------------------------------------------------------------------- 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: 4.9990 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... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN F 74 ASN ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** M 234 ASN N 136 HIS ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3738 r_free = 0.3738 target = 0.084754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059649 restraints weight = 97529.345| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.62 r_work: 0.2955 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26356 Z= 0.160 Angle : 0.688 9.070 35731 Z= 0.373 Chirality : 0.046 0.318 3866 Planarity : 0.005 0.100 4570 Dihedral : 13.913 168.189 4057 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.75 % Allowed : 7.47 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.15), residues: 3062 helix: 0.76 (0.15), residues: 1168 sheet: -0.62 (0.23), residues: 523 loop : -1.99 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 278 TYR 0.021 0.002 TYR K 250 PHE 0.024 0.002 PHE H 111 TRP 0.025 0.002 TRP L 77 HIS 0.011 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (26356) covalent geometry : angle 0.68776 / 0.37 (35731) hydrogen bonds : bond 0.05649 / 3.73 ( 1028) hydrogen bonds : angle 5.71688 / 4.08 ( 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 286 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 1.020 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: 0.8674 (tmm) cc_final: 0.7107 (tmm) REVERT: C 103 CYS cc_start: 0.9336 (m) cc_final: 0.8881 (p) REVERT: C 209 MET cc_start: 0.8536 (tpp) cc_final: 0.8310 (tpp) REVERT: C 271 LYS cc_start: 0.9467 (pptt) cc_final: 0.9172 (pptt) REVERT: C 272 ASN cc_start: 0.9397 (m110) cc_final: 0.9191 (m110) REVERT: D 141 MET cc_start: 0.8930 (mtm) cc_final: 0.8520 (pmm) REVERT: D 150 MET cc_start: 0.8891 (tpt) cc_final: 0.8586 (tpp) REVERT: E 264 TYR cc_start: 0.7849 (m-10) cc_final: 0.7548 (m-10) REVERT: F 116 MET cc_start: 0.9389 (mpp) cc_final: 0.8686 (mpp) REVERT: G 116 MET cc_start: 0.8872 (mpp) cc_final: 0.8251 (mpp) REVERT: G 209 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4956 (ttt) REVERT: H 77 TRP cc_start: 0.8597 (t60) cc_final: 0.8215 (t60) REVERT: H 116 ASP cc_start: 0.9260 (p0) cc_final: 0.8993 (t0) REVERT: I 41 PHE cc_start: 0.9136 (t80) cc_final: 0.8896 (t80) REVERT: I 68 PHE cc_start: 0.7661 (t80) cc_final: 0.7235 (t80) REVERT: I 88 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8506 (ttp80) REVERT: K 288 MET cc_start: 0.9529 (mmp) cc_final: 0.9307 (mmp) REVERT: K 300 HIS cc_start: 0.8821 (m90) cc_final: 0.8005 (m-70) REVERT: K 327 LEU cc_start: 0.9427 (mm) cc_final: 0.8815 (pp) REVERT: L 9 ASP cc_start: 0.8649 (m-30) cc_final: 0.8432 (m-30) REVERT: L 56 MET cc_start: 0.8620 (mmp) cc_final: 0.8005 (ttt) REVERT: A 11 LYS cc_start: 0.8486 (tptt) cc_final: 0.8186 (tppt) outliers start: 20 outliers final: 8 residues processed: 275 average time/residue: 0.1753 time to fit residues: 76.3249 Evaluate side-chains 233 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain N residue 98 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 2 optimal weight: 1.9990 chunk 288 optimal weight: 0.0010 chunk 8 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.084968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059837 restraints weight = 98685.451| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.73 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26356 Z= 0.144 Angle : 0.615 9.666 35731 Z= 0.334 Chirality : 0.044 0.300 3866 Planarity : 0.004 0.070 4570 Dihedral : 13.793 167.718 4057 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.06 % Allowed : 11.46 % Favored : 87.48 % 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: 0.97 (0.15), residues: 1173 sheet: -0.42 (0.22), residues: 518 loop : -1.91 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 278 TYR 0.024 0.002 TYR G 178 PHE 0.028 0.001 PHE H 122 TRP 0.010 0.001 TRP N 43 HIS 0.008 0.001 HIS F 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26356) covalent geometry : angle 0.61508 / 0.33 (35731) hydrogen bonds : bond 0.04958 / 3.26 ( 1028) hydrogen bonds : angle 5.32719 / 3.83 ( 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 272 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 1.013 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: symmetry clash REVERT: B 209 MET cc_start: 0.8377 (tmm) cc_final: 0.6796 (tmm) REVERT: C 103 CYS cc_start: 0.8751 (m) cc_final: 0.8378 (m) REVERT: C 167 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8240 (mmp) REVERT: C 209 MET cc_start: 0.8513 (tpp) cc_final: 0.8216 (tpp) REVERT: D 77 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8935 (tt) REVERT: E 150 MET cc_start: 0.8717 (tpp) cc_final: 0.8481 (tpp) REVERT: E 167 MET cc_start: 0.7558 (mmm) cc_final: 0.7297 (mmm) REVERT: E 209 MET cc_start: 0.8294 (mmm) cc_final: 0.7843 (tpp) REVERT: F 116 MET cc_start: 0.9419 (mpp) cc_final: 0.8884 (mpp) REVERT: F 178 TYR cc_start: 0.8929 (m-80) cc_final: 0.8723 (m-80) REVERT: F 209 MET cc_start: 0.9123 (tmm) cc_final: 0.8175 (ttp) REVERT: G 178 TYR cc_start: 0.8528 (m-80) cc_final: 0.8245 (m-80) REVERT: H 77 TRP cc_start: 0.8541 (t60) cc_final: 0.8329 (t60) REVERT: H 89 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6738 (t80) REVERT: H 116 ASP cc_start: 0.9318 (p0) cc_final: 0.8995 (t0) REVERT: I 39 ARG cc_start: 0.8880 (mtp180) cc_final: 0.8453 (ttm170) REVERT: I 40 TYR cc_start: 0.8544 (m-10) cc_final: 0.8043 (m-10) REVERT: I 65 LYS cc_start: 0.9386 (pptt) cc_final: 0.9112 (pptt) REVERT: I 68 PHE cc_start: 0.7659 (t80) cc_final: 0.7028 (t80) REVERT: I 88 ARG cc_start: 0.8881 (tmm-80) cc_final: 0.8523 (ttp80) REVERT: J 22 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9036 (tm-30) REVERT: J 68 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: K 300 HIS cc_start: 0.8675 (m90) cc_final: 0.7875 (m-70) REVERT: K 327 LEU cc_start: 0.9381 (mm) cc_final: 0.8717 (pp) REVERT: L 9 ASP cc_start: 0.8702 (m-30) cc_final: 0.8461 (m-30) outliers start: 28 outliers final: 14 residues processed: 258 average time/residue: 0.1704 time to fit residues: 69.8676 Evaluate side-chains 242 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 77 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 51 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 98 VAL 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 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: 5.9990 chunk 151 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 75 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN ** N 103 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 = 0.3746 r_free = 0.3746 target = 0.084906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059771 restraints weight = 99598.080| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.70 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1831 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 : 0.604 9.036 35731 Z= 0.327 Chirality : 0.043 0.281 3866 Planarity : 0.004 0.070 4570 Dihedral : 13.725 166.836 4057 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.62 % Allowed : 13.24 % Favored : 85.14 % 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: -0.68 (0.15), residues: 3062 helix: 1.06 (0.16), residues: 1174 sheet: -0.33 (0.23), residues: 514 loop : -1.89 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 80 TYR 0.025 0.002 TYR N 139 PHE 0.026 0.001 PHE H 111 TRP 0.008 0.001 TRP H 77 HIS 0.006 0.001 HIS D 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (26356) covalent geometry : angle 0.60355 / 0.33 (35731) hydrogen bonds : bond 0.04622 / 3.04 ( 1028) hydrogen bonds : angle 5.16792 / 3.72 ( 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 277 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 1.062 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: 0.8392 (tmm) cc_final: 0.6797 (tmm) REVERT: C 85 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8325 (p0) REVERT: C 103 CYS cc_start: 0.8736 (m) cc_final: 0.8361 (m) REVERT: C 167 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8122 (mmp) REVERT: C 209 MET cc_start: 0.8459 (tpp) cc_final: 0.8137 (tpp) REVERT: C 255 VAL cc_start: 0.8710 (m) cc_final: 0.8476 (p) REVERT: D 77 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8960 (tt) REVERT: E 167 MET cc_start: 0.7537 (mmm) cc_final: 0.7278 (mmm) REVERT: E 209 MET cc_start: 0.8258 (tmm) cc_final: 0.7468 (tpp) REVERT: F 116 MET cc_start: 0.9438 (mpp) cc_final: 0.8599 (mpp) REVERT: F 178 TYR cc_start: 0.8954 (m-80) cc_final: 0.8702 (m-80) REVERT: F 209 MET cc_start: 0.9100 (tmm) cc_final: 0.8129 (ttp) REVERT: G 116 MET cc_start: 0.8758 (mpp) cc_final: 0.7963 (mpp) REVERT: G 178 TYR cc_start: 0.8468 (m-80) cc_final: 0.8074 (m-80) REVERT: H 77 TRP cc_start: 0.8621 (t60) cc_final: 0.8402 (t60) REVERT: H 89 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6820 (t80) REVERT: H 116 ASP cc_start: 0.9360 (p0) cc_final: 0.8950 (t0) REVERT: I 39 ARG cc_start: 0.8946 (mtp180) cc_final: 0.8662 (ttm170) REVERT: I 40 TYR cc_start: 0.8622 (m-10) cc_final: 0.8356 (m-10) REVERT: I 65 LYS cc_start: 0.9342 (pptt) cc_final: 0.9082 (pptt) REVERT: I 68 PHE cc_start: 0.7832 (t80) cc_final: 0.7106 (t80) REVERT: I 88 ARG cc_start: 0.8885 (tmm-80) cc_final: 0.8549 (tmm-80) REVERT: J 68 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: K 300 HIS cc_start: 0.8480 (m90) cc_final: 0.7599 (m-70) REVERT: K 327 LEU cc_start: 0.9381 (mm) cc_final: 0.8714 (pp) REVERT: L 9 ASP cc_start: 0.8691 (m-30) cc_final: 0.8453 (m-30) REVERT: L 56 MET cc_start: 0.8531 (mmp) cc_final: 0.7615 (ttt) REVERT: A 47 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8845 (tp30) outliers start: 43 outliers final: 21 residues processed: 260 average time/residue: 0.1676 time to fit residues: 70.6520 Evaluate side-chains 246 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 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 H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET 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 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 363 MET 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 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: 4.9990 chunk 134 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.057970 restraints weight = 101573.973| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.62 r_work: 0.2911 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26356 Z= 0.265 Angle : 0.674 9.688 35731 Z= 0.364 Chirality : 0.045 0.461 3866 Planarity : 0.005 0.061 4570 Dihedral : 13.760 169.509 4057 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.07 % Allowed : 14.86 % Favored : 83.07 % 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: -0.79 (0.15), residues: 3062 helix: 1.03 (0.15), residues: 1175 sheet: -0.54 (0.23), residues: 530 loop : -1.97 (0.15), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 80 TYR 0.029 0.002 TYR N 139 PHE 0.028 0.002 PHE H 111 TRP 0.008 0.001 TRP C 203 HIS 0.008 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (26356) covalent geometry : angle 0.67394 / 0.36 (35731) hydrogen bonds : bond 0.04922 / 3.24 ( 1028) hydrogen bonds : angle 5.34441 / 3.84 ( 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 285 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.030 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: 0.9332 (m) cc_final: 0.9065 (m) REVERT: C 167 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8388 (mmp) REVERT: C 209 MET cc_start: 0.8705 (tpp) cc_final: 0.8495 (tpp) REVERT: C 255 VAL cc_start: 0.8839 (m) cc_final: 0.8637 (p) REVERT: D 25 ASP cc_start: 0.8485 (m-30) cc_final: 0.8079 (m-30) REVERT: D 77 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9000 (tt) REVERT: D 150 MET cc_start: 0.8646 (tpp) cc_final: 0.8431 (ttt) REVERT: E 125 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9211 (m) REVERT: E 167 MET cc_start: 0.8018 (mmm) cc_final: 0.7755 (mmm) REVERT: F 116 MET cc_start: 0.9420 (mpp) cc_final: 0.8358 (mpp) REVERT: F 209 MET cc_start: 0.9068 (tmm) cc_final: 0.8242 (ttp) REVERT: G 178 TYR cc_start: 0.8660 (m-80) cc_final: 0.8316 (m-80) REVERT: G 209 MET cc_start: 0.5086 (tmm) cc_final: 0.4741 (ttt) REVERT: H 89 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7071 (t80) REVERT: I 39 ARG cc_start: 0.8870 (mtp180) cc_final: 0.8591 (ttm170) REVERT: I 40 TYR cc_start: 0.8643 (m-10) cc_final: 0.8436 (m-10) REVERT: I 65 LYS cc_start: 0.9213 (pptt) cc_final: 0.8855 (ptmm) REVERT: I 68 PHE cc_start: 0.7816 (t80) cc_final: 0.7158 (t80) REVERT: I 88 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8542 (tmm-80) REVERT: M 31 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7133 (mtt-85) REVERT: K 1 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7156 (tpt) REVERT: K 300 HIS cc_start: 0.8717 (m90) cc_final: 0.8172 (m-70) REVERT: L 9 ASP cc_start: 0.8534 (m-30) cc_final: 0.8320 (m-30) REVERT: A 47 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8869 (tp30) REVERT: A 50 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8273 (tm-30) outliers start: 55 outliers final: 30 residues processed: 262 average time/residue: 0.1695 time to fit residues: 71.1614 Evaluate side-chains 253 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 147 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 125 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 H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET 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 1 MET 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 363 MET 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 34 GLU 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: 0.5980 chunk 155 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN H 123 ASN M 222 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** 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 = 0.3711 r_free = 0.3711 target = 0.083393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058251 restraints weight = 101194.510| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.65 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1919 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= 0.215 Angle : 0.647 12.213 35731 Z= 0.348 Chirality : 0.044 0.369 3866 Planarity : 0.004 0.045 4570 Dihedral : 13.748 168.812 4057 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.41 % Allowed : 15.57 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.75 (0.15), residues: 3062 helix: 1.08 (0.16), residues: 1174 sheet: -0.63 (0.22), residues: 535 loop : -1.92 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 80 TYR 0.029 0.002 TYR N 139 PHE 0.027 0.002 PHE H 111 TRP 0.018 0.002 TRP H 77 HIS 0.009 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (26356) covalent geometry : angle 0.64719 / 0.35 (35731) hydrogen bonds : bond 0.04695 / 3.10 ( 1028) hydrogen bonds : angle 5.19461 / 3.73 ( 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 287 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 223 time to evaluate : 1.053 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: 0.8666 (m) cc_final: 0.8310 (m) REVERT: C 167 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8179 (mmp) REVERT: D 25 ASP cc_start: 0.8343 (m-30) cc_final: 0.7951 (m-30) REVERT: D 77 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8940 (tt) REVERT: D 150 MET cc_start: 0.8512 (tpp) cc_final: 0.8172 (ttt) REVERT: E 125 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8914 (m) REVERT: E 167 MET cc_start: 0.7673 (mmm) cc_final: 0.7335 (mmm) REVERT: E 209 MET cc_start: 0.7275 (tpp) cc_final: 0.6702 (tpp) REVERT: F 116 MET cc_start: 0.9444 (mpp) cc_final: 0.8577 (mpp) REVERT: F 209 MET cc_start: 0.9056 (tmm) cc_final: 0.8353 (ttp) REVERT: G 178 TYR cc_start: 0.8714 (m-80) cc_final: 0.8369 (m-80) REVERT: H 89 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7124 (t80) REVERT: I 39 ARG cc_start: 0.8960 (mtp180) cc_final: 0.8740 (ttm170) REVERT: I 40 TYR cc_start: 0.8562 (m-10) cc_final: 0.8349 (m-10) REVERT: I 65 LYS cc_start: 0.9308 (pptt) cc_final: 0.8928 (ptmm) REVERT: I 68 PHE cc_start: 0.7819 (t80) cc_final: 0.7116 (t80) REVERT: I 88 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8551 (tmm-80) REVERT: M 31 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6911 (mtt-85) REVERT: K 1 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7149 (tpt) REVERT: K 300 HIS cc_start: 0.8569 (m90) cc_final: 0.8111 (m-70) REVERT: L 9 ASP cc_start: 0.8657 (m-30) cc_final: 0.8421 (m-30) REVERT: L 56 MET cc_start: 0.8557 (mmp) cc_final: 0.7566 (ttt) REVERT: A 47 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8892 (tp30) REVERT: A 50 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8294 (tm-30) outliers start: 64 outliers final: 33 residues processed: 265 average time/residue: 0.1586 time to fit residues: 67.7725 Evaluate side-chains 257 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 167 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 125 VAL 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 H residue 51 VAL Chi-restraints excluded: chain H residue 89 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 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET 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 1 MET 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 363 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 263 optimal weight: 0.0010 chunk 290 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 253 optimal weight: 0.0980 chunk 254 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN H 120 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.084050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058898 restraints weight = 99836.302| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.66 r_work: 0.2999 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26356 Z= 0.156 Angle : 0.613 13.520 35731 Z= 0.328 Chirality : 0.043 0.414 3866 Planarity : 0.004 0.056 4570 Dihedral : 13.713 167.702 4057 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.07 % Allowed : 16.37 % Favored : 81.56 % 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: -0.62 (0.15), residues: 3062 helix: 1.18 (0.16), residues: 1176 sheet: -0.45 (0.23), residues: 513 loop : -1.87 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 80 TYR 0.027 0.002 TYR L 40 PHE 0.029 0.001 PHE H 111 TRP 0.017 0.001 TRP H 77 HIS 0.008 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (26356) covalent geometry : angle 0.61344 / 0.33 (35731) hydrogen bonds : bond 0.04430 / 2.91 ( 1028) hydrogen bonds : angle 5.01517 / 3.61 ( 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 280 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.678 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: 0.8785 (tmm) cc_final: 0.7103 (tmm) REVERT: C 103 CYS cc_start: 0.9275 (m) cc_final: 0.9021 (m) REVERT: C 209 MET cc_start: 0.8537 (tpp) cc_final: 0.8333 (tpp) REVERT: D 77 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8890 (tt) REVERT: D 150 MET cc_start: 0.8768 (tpp) cc_final: 0.8282 (ttt) REVERT: E 167 MET cc_start: 0.7807 (mmm) cc_final: 0.7505 (mmm) REVERT: E 209 MET cc_start: 0.7715 (tpp) cc_final: 0.7219 (tpp) REVERT: F 116 MET cc_start: 0.9471 (mpp) cc_final: 0.8462 (mpp) REVERT: F 209 MET cc_start: 0.9074 (tmm) cc_final: 0.8299 (ttp) REVERT: G 116 MET cc_start: 0.8684 (mpp) cc_final: 0.7950 (mpp) REVERT: G 178 TYR cc_start: 0.8713 (m-80) cc_final: 0.8360 (m-80) REVERT: H 89 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6994 (t80) REVERT: I 39 ARG cc_start: 0.8866 (mtp180) cc_final: 0.8635 (ttm170) REVERT: I 65 LYS cc_start: 0.9123 (pptt) cc_final: 0.8700 (ptmm) REVERT: I 68 PHE cc_start: 0.7811 (t80) cc_final: 0.7135 (t80) REVERT: I 88 ARG cc_start: 0.8889 (tmm-80) cc_final: 0.8524 (tmm-80) REVERT: J 27 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8511 (mp0) REVERT: M 31 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6981 (mtt-85) REVERT: N 171 MET cc_start: 0.7252 (tpt) cc_final: 0.6825 (mmm) REVERT: K 1 MET cc_start: 0.7664 (tpt) cc_final: 0.7239 (tpt) REVERT: K 11 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.9075 (mt0) REVERT: K 300 HIS cc_start: 0.8688 (m90) cc_final: 0.8350 (m-70) REVERT: L 40 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: L 56 MET cc_start: 0.8366 (mmp) cc_final: 0.7751 (ttt) outliers start: 55 outliers final: 36 residues processed: 266 average time/residue: 0.1651 time to fit residues: 69.9937 Evaluate side-chains 256 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE 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 222 ASN Chi-restraints excluded: chain F residue 227 TYR 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 38 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain M residue 31 ARG 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 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET 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 281 LEU Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 363 MET Chi-restraints excluded: chain K residue 471 LEU 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 34 GLU 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: 2.9990 chunk 114 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 111 optimal weight: 0.0170 chunk 64 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 HIS G 214 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054656 restraints weight = 107506.074| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 4.67 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 26356 Z= 0.275 Angle : 0.694 13.080 35731 Z= 0.371 Chirality : 0.046 0.419 3866 Planarity : 0.005 0.059 4570 Dihedral : 13.731 169.550 4057 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.19 % Allowed : 16.59 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.10 (0.15), residues: 1176 sheet: -0.68 (0.23), residues: 529 loop : -1.93 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 80 TYR 0.030 0.002 TYR N 139 PHE 0.032 0.002 PHE H 111 TRP 0.012 0.002 TRP H 77 HIS 0.009 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 (26356) covalent geometry : angle 0.69396 / 0.37 (35731) hydrogen bonds : bond 0.04802 / 3.16 ( 1028) hydrogen bonds : angle 5.27059 / 3.78 ( 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 276 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 MET cc_start: 0.8678 (mmt) cc_final: 0.8415 (mmm) REVERT: D 77 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8945 (tt) REVERT: D 150 MET cc_start: 0.8648 (tpp) cc_final: 0.8262 (ttt) REVERT: E 167 MET cc_start: 0.7546 (mmm) cc_final: 0.7327 (mmm) REVERT: E 209 MET cc_start: 0.7358 (tpp) cc_final: 0.6820 (tpp) REVERT: F 116 MET cc_start: 0.9421 (mpp) cc_final: 0.8506 (mpp) REVERT: F 178 TYR cc_start: 0.8983 (m-80) cc_final: 0.8583 (m-80) REVERT: F 209 MET cc_start: 0.8971 (tmm) cc_final: 0.8258 (ttp) REVERT: G 116 MET cc_start: 0.8823 (mpp) cc_final: 0.8074 (mpp) REVERT: G 178 TYR cc_start: 0.8690 (m-80) cc_final: 0.8266 (m-80) REVERT: H 71 ARG cc_start: 0.8556 (mmp80) cc_final: 0.8351 (mmm160) REVERT: H 77 TRP cc_start: 0.7941 (t60) cc_final: 0.7646 (t60) REVERT: H 89 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7201 (t80) REVERT: I 39 ARG cc_start: 0.8947 (mtp180) cc_final: 0.8710 (ttm170) REVERT: I 65 LYS cc_start: 0.9216 (pptt) cc_final: 0.8766 (ptmm) REVERT: I 68 PHE cc_start: 0.7904 (t80) cc_final: 0.7230 (t80) REVERT: I 88 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8510 (tmm-80) REVERT: M 31 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6958 (mtt-85) REVERT: N 171 MET cc_start: 0.7184 (tpt) cc_final: 0.6835 (mmm) REVERT: K 1 MET cc_start: 0.7955 (tpt) cc_final: 0.7583 (tpt) REVERT: K 11 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.9124 (mt0) REVERT: K 300 HIS cc_start: 0.8572 (m90) cc_final: 0.8213 (m-70) REVERT: L 40 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8962 (m-80) REVERT: L 56 MET cc_start: 0.8298 (mmp) cc_final: 0.7848 (ttt) outliers start: 58 outliers final: 45 residues processed: 260 average time/residue: 0.1646 time to fit residues: 68.2503 Evaluate side-chains 263 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain B residue 222 ASN 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 D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 118 THR 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 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 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 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 74 MET 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 240 PHE 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 363 MET Chi-restraints excluded: chain K residue 471 LEU 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 34 GLU 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: 0.5980 chunk 205 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 2 optimal weight: 0.0670 chunk 140 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 HIS G 214 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN ** H 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** 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 = 0.3729 r_free = 0.3729 target = 0.084284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059026 restraints weight = 99929.877| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.70 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26356 Z= 0.159 Angle : 0.640 15.538 35731 Z= 0.337 Chirality : 0.044 0.376 3866 Planarity : 0.004 0.080 4570 Dihedral : 13.701 167.539 4057 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.38 % Allowed : 16.93 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.15), residues: 3062 helix: 1.20 (0.16), residues: 1175 sheet: -0.48 (0.23), residues: 514 loop : -1.89 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 80 TYR 0.027 0.002 TYR L 40 PHE 0.032 0.002 PHE H 111 TRP 0.014 0.001 TRP H 77 HIS 0.020 0.001 HIS G 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (26356) covalent geometry : angle 0.63972 / 0.34 (35731) hydrogen bonds : bond 0.04369 / 2.89 ( 1028) hydrogen bonds : angle 4.98971 / 3.59 ( 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 287 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 1.039 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: 0.8511 (tmm) cc_final: 0.6834 (tmm) REVERT: D 77 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8880 (tt) REVERT: D 150 MET cc_start: 0.8501 (tpp) cc_final: 0.8153 (ttt) REVERT: E 167 MET cc_start: 0.7427 (mmm) cc_final: 0.7215 (mmm) REVERT: F 116 MET cc_start: 0.9436 (mpp) cc_final: 0.8591 (mpp) REVERT: F 178 TYR cc_start: 0.8969 (m-80) cc_final: 0.8545 (m-80) REVERT: F 209 MET cc_start: 0.8990 (tmm) cc_final: 0.8737 (tmm) REVERT: G 105 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8918 (tpp80) REVERT: G 116 MET cc_start: 0.8789 (mpp) cc_final: 0.8052 (mpp) REVERT: G 178 TYR cc_start: 0.8714 (m-80) cc_final: 0.8355 (m-80) REVERT: H 71 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8351 (mmm160) REVERT: H 77 TRP cc_start: 0.7977 (t60) cc_final: 0.7677 (t60) REVERT: H 89 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7067 (t80) REVERT: I 39 ARG cc_start: 0.8928 (mtp180) cc_final: 0.8701 (ttm170) REVERT: I 40 TYR cc_start: 0.8530 (m-10) cc_final: 0.8298 (m-10) REVERT: I 41 PHE cc_start: 0.8912 (t80) cc_final: 0.8664 (t80) REVERT: I 65 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8806 (ptmm) REVERT: I 68 PHE cc_start: 0.7907 (t80) cc_final: 0.7221 (t80) REVERT: I 88 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8608 (tmm-80) REVERT: J 27 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8610 (mp0) REVERT: J 68 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: M 31 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6893 (mtt-85) REVERT: N 171 MET cc_start: 0.7199 (tpt) cc_final: 0.6928 (mmm) REVERT: N 195 CYS cc_start: 0.9411 (t) cc_final: 0.9191 (p) REVERT: K 1 MET cc_start: 0.7640 (tpt) cc_final: 0.7165 (tpt) REVERT: K 11 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.9131 (mt0) REVERT: K 300 HIS cc_start: 0.8532 (m90) cc_final: 0.8210 (m-70) REVERT: L 40 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: L 56 MET cc_start: 0.8601 (mmp) cc_final: 0.7597 (ttt) outliers start: 63 outliers final: 47 residues processed: 268 average time/residue: 0.1684 time to fit residues: 72.0045 Evaluate side-chains 270 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 222 ASN Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 118 THR 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 73 LEU Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 65 LYS 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 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 74 MET 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 363 MET Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU 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 34 GLU 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: 7.9990 chunk 290 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 308 optimal weight: 10.0000 chunk 204 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 GLN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.081645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056932 restraints weight = 105123.637| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.70 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26356 Z= 0.129 Angle : 0.638 14.850 35731 Z= 0.332 Chirality : 0.043 0.415 3866 Planarity : 0.004 0.085 4570 Dihedral : 13.647 166.001 4057 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.96 % Allowed : 17.46 % Favored : 80.58 % 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: -0.54 (0.15), residues: 3062 helix: 1.21 (0.16), residues: 1181 sheet: -0.37 (0.23), residues: 516 loop : -1.80 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 80 TYR 0.025 0.001 TYR L 40 PHE 0.031 0.001 PHE H 111 TRP 0.015 0.002 TRP H 77 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (26356) covalent geometry : angle 0.63831 / 0.33 (35731) hydrogen bonds : bond 0.04006 / 2.64 ( 1028) hydrogen bonds : angle 4.81543 / 3.47 ( 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 283 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.002 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: 0.8429 (tmm) cc_final: 0.6832 (tmm) REVERT: C 167 MET cc_start: 0.8985 (mmm) cc_final: 0.8594 (mmm) REVERT: D 77 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8847 (tt) REVERT: D 150 MET cc_start: 0.8319 (tpp) cc_final: 0.8029 (ttt) REVERT: E 116 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8961 (ptp) REVERT: E 167 MET cc_start: 0.7406 (mmm) cc_final: 0.7081 (mmm) REVERT: E 209 MET cc_start: 0.7665 (tpp) cc_final: 0.7337 (tpp) REVERT: F 116 MET cc_start: 0.9483 (mpp) cc_final: 0.8651 (mpp) REVERT: F 178 TYR cc_start: 0.8971 (m-80) cc_final: 0.8556 (m-80) REVERT: F 209 MET cc_start: 0.9054 (tmm) cc_final: 0.8263 (ttp) REVERT: G 105 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8959 (tpp80) REVERT: G 116 MET cc_start: 0.8831 (mpp) cc_final: 0.8081 (mpp) REVERT: G 178 TYR cc_start: 0.8618 (m-80) cc_final: 0.8278 (m-80) REVERT: H 71 ARG cc_start: 0.8619 (mmp80) cc_final: 0.8400 (mmm160) REVERT: H 77 TRP cc_start: 0.7940 (t60) cc_final: 0.7629 (t60) REVERT: H 89 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7155 (t80) REVERT: H 124 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: I 39 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8575 (ttm170) REVERT: I 40 TYR cc_start: 0.8491 (m-10) cc_final: 0.8210 (m-10) REVERT: I 41 PHE cc_start: 0.8907 (t80) cc_final: 0.8695 (t80) REVERT: I 65 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8705 (ptmm) REVERT: I 68 PHE cc_start: 0.8013 (t80) cc_final: 0.7374 (t80) REVERT: I 88 ARG cc_start: 0.8872 (tmm-80) cc_final: 0.8477 (ttp80) REVERT: J 27 GLU cc_start: 0.9411 (mm-30) cc_final: 0.8622 (mp0) REVERT: J 57 ARG cc_start: 0.8980 (mtp85) cc_final: 0.8668 (mmm-85) REVERT: M 31 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6940 (mtt-85) REVERT: N 171 MET cc_start: 0.7177 (tpt) cc_final: 0.6898 (mmm) REVERT: N 195 CYS cc_start: 0.9439 (t) cc_final: 0.9152 (p) REVERT: K 1 MET cc_start: 0.7450 (tpt) cc_final: 0.6907 (tpt) REVERT: K 11 GLN cc_start: 0.9466 (OUTLIER) cc_final: 0.9098 (mt0) REVERT: K 300 HIS cc_start: 0.8498 (m90) cc_final: 0.8174 (m-70) REVERT: K 325 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7672 (t80) REVERT: L 40 TYR cc_start: 0.9204 (m-80) cc_final: 0.8926 (m-80) REVERT: L 56 MET cc_start: 0.8368 (mmp) cc_final: 0.7946 (ttt) outliers start: 52 outliers final: 37 residues processed: 268 average time/residue: 0.1704 time to fit residues: 72.2722 Evaluate side-chains 266 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 103 CYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 118 THR 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 105 ARG Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 65 LYS 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 268 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET 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 363 MET Chi-restraints excluded: chain K residue 426 GLU Chi-restraints excluded: chain K residue 471 LEU Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 12 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 275 optimal weight: 4.9990 chunk 5 optimal weight: 0.0170 chunk 185 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 277 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS ** K 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.084505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059361 restraints weight = 99599.097| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.69 r_work: 0.3016 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26356 Z= 0.179 Angle : 0.649 14.544 35731 Z= 0.339 Chirality : 0.043 0.419 3866 Planarity : 0.004 0.043 4570 Dihedral : 13.607 166.492 4057 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.04 % Allowed : 17.61 % Favored : 80.35 % 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: 1.27 (0.16), residues: 1181 sheet: -0.41 (0.23), residues: 520 loop : -1.80 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 39 TYR 0.025 0.002 TYR L 40 PHE 0.030 0.002 PHE H 111 TRP 0.010 0.001 TRP H 77 HIS 0.007 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (26356) covalent geometry : angle 0.64925 / 0.34 (35731) hydrogen bonds : bond 0.04168 / 2.75 ( 1028) hydrogen bonds : angle 4.89129 / 3.52 ( 3009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6595.28 seconds wall clock time: 113 minutes 54.38 seconds (6834.38 seconds total)