Starting phenix.real_space_refine on Sun Jun 22 08:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9s_29877/06_2025/8g9s_29877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9s_29877/06_2025/8g9s_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_29877/06_2025/8g9s_29877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9s_29877/06_2025/8g9s_29877.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9s_29877/06_2025/8g9s_29877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9s_29877/06_2025/8g9s_29877.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.53, per 1000 atoms: 0.56 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: 6.27 Conformation dependent library (CDL) restraints added in 3.1 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: 7.58 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: 7.87 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6747 1.33 - 1.45: 5476 1.45 - 1.57: 13865 1.57 - 1.70: 83 1.70 - 1.82: 185 Bond restraints: 26356 Sorted by residual: bond pdb=" CA ASP C 213 " pdb=" CB ASP C 213 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.35e-02 5.49e+03 6.37e+00 bond pdb=" CG1 ILE M 147 " pdb=" CD1 ILE M 147 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.87e+00 bond pdb=" CA ASP C 8 " pdb=" CB ASP C 8 " ideal model delta sigma weight residual 1.534 1.496 0.037 1.72e-02 3.38e+03 4.74e+00 bond pdb=" CA GLY B 22 " pdb=" C GLY B 22 " ideal model delta sigma weight residual 1.520 1.506 0.014 7.30e-03 1.88e+04 3.70e+00 bond pdb=" CB VAL C 50 " pdb=" CG2 VAL C 50 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.38e+00 ... (remaining 26351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 33991 1.78 - 3.56: 1483 3.56 - 5.33: 214 5.33 - 7.11: 34 7.11 - 8.89: 9 Bond angle restraints: 35731 Sorted by residual: angle pdb=" C ARG B 224 " pdb=" N GLY B 225 " pdb=" CA GLY B 225 " ideal model delta sigma weight residual 122.33 119.18 3.15 7.30e-01 1.88e+00 1.86e+01 angle pdb=" N VAL G 258 " pdb=" CA VAL G 258 " pdb=" C VAL G 258 " ideal model delta sigma weight residual 106.21 109.99 -3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" C ASP M 157 " pdb=" N ALA M 158 " pdb=" CA ALA M 158 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CB ARG D 259 " pdb=" CG ARG D 259 " pdb=" CD ARG D 259 " ideal model delta sigma weight residual 111.30 119.09 -7.79 2.30e+00 1.89e-01 1.15e+01 angle pdb=" CA MET E 209 " pdb=" CB MET E 209 " pdb=" CG MET E 209 " ideal model delta sigma weight residual 114.10 107.56 6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 35726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15483 35.76 - 71.53: 345 71.53 - 107.29: 53 107.29 - 143.05: 3 143.05 - 178.81: 3 Dihedral angle restraints: 15887 sinusoidal: 6974 harmonic: 8913 Sorted by residual: dihedral pdb=" O4' C O 14 " pdb=" C1' C O 14 " pdb=" N1 C O 14 " pdb=" C2 C O 14 " ideal model delta sinusoidal sigma weight residual 200.00 42.17 157.83 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' C O 38 " pdb=" C1' C O 38 " pdb=" N1 C O 38 " pdb=" C2 C O 38 " ideal model delta sinusoidal sigma weight residual 200.00 53.15 146.85 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C O 8 " pdb=" C1' C O 8 " pdb=" N1 C O 8 " pdb=" C2 C O 8 " ideal model delta sinusoidal sigma weight residual 200.00 66.11 133.89 1 1.50e+01 4.44e-03 7.22e+01 ... (remaining 15884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3195 0.063 - 0.125: 605 0.125 - 0.188: 62 0.188 - 0.251: 3 0.251 - 0.314: 1 Chirality restraints: 3866 Sorted by residual: chirality pdb=" C3' U O 24 " pdb=" C4' U O 24 " pdb=" O3' U O 24 " pdb=" C2' U O 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB THR K 279 " pdb=" CA THR K 279 " pdb=" OG1 THR K 279 " pdb=" CG2 THR K 279 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' C O 31 " pdb=" O4' C O 31 " pdb=" C2' C O 31 " pdb=" N1 C O 31 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 3863 not shown) Planarity restraints: 4570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 77 " -0.021 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP L 77 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP L 77 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 77 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 77 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP L 77 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 47 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO H 48 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 127 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO D 128 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " -0.033 5.00e-02 4.00e+02 ... (remaining 4567 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 540 2.61 - 3.18: 25668 3.18 - 3.75: 40805 3.75 - 4.33: 55110 4.33 - 4.90: 86984 Nonbonded interactions: 209107 Sorted by model distance: nonbonded pdb=" OG SER M 195 " pdb=" OD1 ASN M 197 " model vdw 2.037 3.040 nonbonded pdb=" OD2 ASP B 237 " pdb=" OG1 THR B 276 " model vdw 2.086 3.040 nonbonded pdb=" NH2 ARG B 51 " pdb=" OP1 U O 13 " model vdw 2.086 3.120 nonbonded pdb=" NH2 ARG E 51 " pdb=" OP1 C O 31 " model vdw 2.094 3.120 nonbonded pdb=" OD2 ASP M 237 " pdb=" OG1 THR M 276 " model vdw 2.097 3.040 ... (remaining 209102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'G' and (resid 2 through 74 or resid 94 through 148 or resid 167 through \ 284)) selection = (chain 'M' and (resid 2 through 148 or resid 167 through 284)) } ncs_group { reference = (chain 'H' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'I' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = (chain 'J' and (resid 2 through 67 or resid 70 through 85 or resid 94 through 12 \ 5)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 58.610 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 26356 Z= 0.351 Angle : 0.851 8.889 35731 Z= 0.488 Chirality : 0.048 0.314 3866 Planarity : 0.005 0.061 4570 Dihedral : 16.325 178.815 10159 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 24.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.058 0.003 TRP L 77 HIS 0.020 0.002 HIS G 62 PHE 0.030 0.003 PHE M 11 TYR 0.027 0.003 TYR H 12 ARG 0.016 0.001 ARG G 280 Details of bonding type rmsd hydrogen bonds : bond 0.17097 ( 1028) hydrogen bonds : angle 7.56728 ( 3009) covalent geometry : bond 0.00760 (26356) covalent geometry : angle 0.85101 (35731) *********************** 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 : 2.710 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: 0.3950 time to fit residues: 160.8909 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 : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN C 85 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 HIS M 124 GLN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.058744 restraints weight = 99121.674| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.64 r_work: 0.2926 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26356 Z= 0.204 Angle : 0.674 7.760 35731 Z= 0.364 Chirality : 0.045 0.283 3866 Planarity : 0.005 0.100 4570 Dihedral : 13.817 169.546 4057 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.83 % Allowed : 7.84 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3062 helix: 0.86 (0.15), residues: 1171 sheet: -0.75 (0.23), residues: 527 loop : -2.04 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 77 HIS 0.006 0.001 HIS F 187 PHE 0.025 0.002 PHE H 111 TYR 0.016 0.002 TYR K 250 ARG 0.008 0.001 ARG K 278 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 1028) hydrogen bonds : angle 5.66727 ( 3009) covalent geometry : bond 0.00450 (26356) covalent geometry : angle 0.67440 (35731) *********************** 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 279 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 CYS cc_start: 0.9303 (m) cc_final: 0.9049 (m) REVERT: C 167 MET cc_start: 0.8956 (mmm) cc_final: 0.8494 (mmp) REVERT: C 255 VAL cc_start: 0.8855 (m) cc_final: 0.8622 (p) REVERT: D 141 MET cc_start: 0.8865 (mtm) cc_final: 0.8484 (pmm) REVERT: D 150 MET cc_start: 0.9099 (tpt) cc_final: 0.8800 (tpp) REVERT: E 150 MET cc_start: 0.9124 (tpp) cc_final: 0.8921 (tpp) REVERT: E 209 MET cc_start: 0.7247 (ttm) cc_final: 0.6392 (tpt) REVERT: F 116 MET cc_start: 0.9387 (mpp) cc_final: 0.8226 (mpp) REVERT: F 209 MET cc_start: 0.8041 (ttp) cc_final: 0.7752 (tmm) REVERT: G 187 HIS cc_start: 0.8736 (m170) cc_final: 0.8511 (m170) REVERT: H 77 TRP cc_start: 0.8555 (t60) cc_final: 0.8158 (t60) REVERT: H 89 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6861 (t80) REVERT: I 55 LEU cc_start: 0.9445 (mt) cc_final: 0.9230 (mt) REVERT: I 68 PHE cc_start: 0.7882 (t80) cc_final: 0.7444 (t80) REVERT: I 88 ARG cc_start: 0.8876 (tmm-80) cc_final: 0.8503 (ttp80) REVERT: N 171 MET cc_start: 0.8916 (tpp) cc_final: 0.8690 (tpt) REVERT: K 300 HIS cc_start: 0.8775 (m90) cc_final: 0.8310 (m-70) REVERT: K 327 LEU cc_start: 0.9421 (mm) cc_final: 0.8817 (pp) REVERT: L 9 ASP cc_start: 0.8586 (m-30) cc_final: 0.8381 (m-30) REVERT: A 24 TYR cc_start: 0.9064 (m-80) cc_final: 0.8862 (m-80) outliers start: 22 outliers final: 11 residues processed: 267 average time/residue: 0.3852 time to fit residues: 160.7756 Evaluate side-chains 229 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain H residue 6 ASN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 363 MET 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 285 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 212 HIS ** 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 313 ASN ** K 518 HIS ** 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 = 0.3665 r_free = 0.3665 target = 0.078315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053836 restraints weight = 107598.293| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.56 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 26356 Z= 0.325 Angle : 0.752 7.530 35731 Z= 0.404 Chirality : 0.047 0.321 3866 Planarity : 0.005 0.097 4570 Dihedral : 13.849 170.085 4057 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.58 % Allowed : 13.12 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 3062 helix: 0.74 (0.15), residues: 1168 sheet: -0.99 (0.22), residues: 555 loop : -2.11 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 203 HIS 0.009 0.001 HIS F 187 PHE 0.032 0.002 PHE M 11 TYR 0.029 0.002 TYR N 139 ARG 0.007 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 1028) hydrogen bonds : angle 5.80122 ( 3009) covalent geometry : bond 0.00715 (26356) covalent geometry : angle 0.75245 (35731) *********************** 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 266 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 2.711 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 102 MET cc_start: 0.8736 (mmt) cc_final: 0.8526 (mmm) REVERT: C 103 CYS cc_start: 0.8667 (m) cc_final: 0.8178 (p) REVERT: D 77 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (tt) REVERT: D 150 MET cc_start: 0.9114 (tpt) cc_final: 0.8805 (tpp) REVERT: D 271 LYS cc_start: 0.9509 (tppt) cc_final: 0.9271 (tppt) REVERT: E 167 MET cc_start: 0.7804 (mmm) cc_final: 0.7585 (mmm) REVERT: E 221 MET cc_start: 0.8312 (mtm) cc_final: 0.8085 (mtm) REVERT: F 116 MET cc_start: 0.9370 (mpp) cc_final: 0.8417 (mpp) REVERT: F 209 MET cc_start: 0.8184 (ttp) cc_final: 0.7728 (tmm) REVERT: G 178 TYR cc_start: 0.8647 (m-80) cc_final: 0.8343 (m-80) REVERT: G 187 HIS cc_start: 0.8890 (m170) cc_final: 0.8642 (m170) REVERT: H 89 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7032 (t80) REVERT: I 39 ARG cc_start: 0.8944 (mtp180) cc_final: 0.8671 (ttp-170) REVERT: I 40 TYR cc_start: 0.8714 (m-10) cc_final: 0.8491 (m-10) REVERT: I 65 LYS cc_start: 0.9314 (pptt) cc_final: 0.9060 (pptt) REVERT: I 68 PHE cc_start: 0.7834 (t80) cc_final: 0.7383 (t80) REVERT: I 88 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.8397 (ttp80) REVERT: J 68 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: M 31 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6967 (mtt-85) REVERT: N 171 MET cc_start: 0.8941 (tpp) cc_final: 0.8696 (tpt) REVERT: K 300 HIS cc_start: 0.8627 (m90) cc_final: 0.7949 (m-70) REVERT: L 56 MET cc_start: 0.8489 (mmp) cc_final: 0.7953 (ttt) outliers start: 42 outliers final: 26 residues processed: 250 average time/residue: 0.3832 time to fit residues: 150.9603 Evaluate side-chains 237 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 2.665 ------------------------------------------------------------------------------- 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 D residue 77 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 42 THR 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 H residue 92 HIS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 165 THR 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 L residue 35 THR Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 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 167 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 18 optimal weight: 0.0040 chunk 180 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN E 21 ASN F 212 HIS F 234 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 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 = 0.3722 r_free = 0.3722 target = 0.080761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055975 restraints weight = 106085.902| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.67 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26356 Z= 0.150 Angle : 0.599 8.570 35731 Z= 0.321 Chirality : 0.042 0.251 3866 Planarity : 0.004 0.065 4570 Dihedral : 13.638 166.975 4057 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.81 % Allowed : 15.16 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3062 helix: 1.17 (0.16), residues: 1176 sheet: -0.61 (0.23), residues: 517 loop : -1.94 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 43 HIS 0.006 0.001 HIS F 187 PHE 0.027 0.001 PHE H 111 TYR 0.015 0.001 TYR H 105 ARG 0.009 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 1028) hydrogen bonds : angle 5.08998 ( 3009) covalent geometry : bond 0.00328 (26356) covalent geometry : angle 0.59892 (35731) *********************** 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 288 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7993 (tt) REVERT: C 102 MET cc_start: 0.8640 (mmt) cc_final: 0.8383 (mmm) REVERT: C 103 CYS cc_start: 0.8662 (m) cc_final: 0.8207 (p) REVERT: C 167 MET cc_start: 0.8958 (mmm) cc_final: 0.8335 (mmp) REVERT: C 209 MET cc_start: 0.8697 (tpp) cc_final: 0.8476 (tpp) REVERT: D 77 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8972 (tt) REVERT: D 150 MET cc_start: 0.8827 (tpt) cc_final: 0.8536 (tpp) REVERT: D 271 LYS cc_start: 0.9498 (tppt) cc_final: 0.9243 (tppt) REVERT: E 167 MET cc_start: 0.7620 (mmm) cc_final: 0.7352 (mmm) REVERT: E 221 MET cc_start: 0.8243 (mtm) cc_final: 0.7989 (mtm) REVERT: F 116 MET cc_start: 0.9466 (mpp) cc_final: 0.8615 (mpp) REVERT: F 209 MET cc_start: 0.8172 (ttp) cc_final: 0.7742 (tmm) REVERT: G 116 MET cc_start: 0.8827 (mpp) cc_final: 0.8000 (mpp) REVERT: G 178 TYR cc_start: 0.8620 (m-80) cc_final: 0.8241 (m-80) REVERT: G 221 MET cc_start: 0.5275 (ptt) cc_final: 0.4981 (ptt) REVERT: H 89 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7230 (t80) REVERT: I 39 ARG cc_start: 0.8967 (mtp180) cc_final: 0.8689 (ttp-170) REVERT: I 55 LEU cc_start: 0.9511 (mt) cc_final: 0.9290 (mt) REVERT: I 65 LYS cc_start: 0.9198 (pptt) cc_final: 0.8735 (ptmm) REVERT: I 88 ARG cc_start: 0.8808 (tmm-80) cc_final: 0.8497 (tmm-80) REVERT: J 68 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: N 81 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8621 (mm) REVERT: N 171 MET cc_start: 0.8823 (tpp) cc_final: 0.8612 (tpt) REVERT: K 1 MET cc_start: 0.7191 (tpt) cc_final: 0.6868 (tpt) REVERT: K 300 HIS cc_start: 0.8550 (m90) cc_final: 0.7975 (m-70) REVERT: L 56 MET cc_start: 0.8335 (mmp) cc_final: 0.7884 (ttt) outliers start: 48 outliers final: 24 residues processed: 274 average time/residue: 0.3787 time to fit residues: 165.8625 Evaluate side-chains 245 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU 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 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 63 LEU Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS 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 15 THR Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 570 PHE Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 280 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 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 = 0.3695 r_free = 0.3695 target = 0.082598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057463 restraints weight = 101601.276| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.60 r_work: 0.2971 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26356 Z= 0.226 Angle : 0.648 7.984 35731 Z= 0.347 Chirality : 0.044 0.281 3866 Planarity : 0.004 0.092 4570 Dihedral : 13.637 168.375 4057 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.75 % Allowed : 15.87 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3062 helix: 1.16 (0.16), residues: 1176 sheet: -0.67 (0.23), residues: 518 loop : -1.96 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 77 HIS 0.007 0.001 HIS F 187 PHE 0.028 0.002 PHE H 111 TYR 0.019 0.002 TYR J 106 ARG 0.006 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 1028) hydrogen bonds : angle 5.20820 ( 3009) covalent geometry : bond 0.00500 (26356) covalent geometry : angle 0.64769 (35731) *********************** 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 296 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8240 (tt) REVERT: C 103 CYS cc_start: 0.9281 (m) cc_final: 0.9048 (m) REVERT: D 141 MET cc_start: 0.8918 (mtt) cc_final: 0.8292 (pmm) REVERT: D 150 MET cc_start: 0.9171 (tpt) cc_final: 0.8862 (tpp) REVERT: D 271 LYS cc_start: 0.9540 (tppt) cc_final: 0.9299 (tppt) REVERT: E 167 MET cc_start: 0.7877 (mmm) cc_final: 0.7606 (mmm) REVERT: F 116 MET cc_start: 0.9426 (mpp) cc_final: 0.8353 (mpp) REVERT: F 209 MET cc_start: 0.8280 (ttp) cc_final: 0.7779 (tmm) REVERT: G 178 TYR cc_start: 0.8734 (m-80) cc_final: 0.8352 (m-80) REVERT: H 89 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7061 (t80) REVERT: I 41 PHE cc_start: 0.9104 (t80) cc_final: 0.8872 (t80) REVERT: I 55 LEU cc_start: 0.9494 (mt) cc_final: 0.9249 (mt) REVERT: I 65 LYS cc_start: 0.9100 (pptt) cc_final: 0.8659 (ptmm) REVERT: I 68 PHE cc_start: 0.8336 (m-10) cc_final: 0.8036 (t80) REVERT: I 88 ARG cc_start: 0.8773 (tmm-80) cc_final: 0.8391 (ttp80) REVERT: J 57 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8242 (mtt-85) REVERT: J 68 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: M 31 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7071 (mtt-85) REVERT: N 81 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8577 (mm) REVERT: K 11 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9040 (mt0) REVERT: K 300 HIS cc_start: 0.8723 (m90) cc_final: 0.8261 (m-70) REVERT: K 325 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7818 (t80) REVERT: L 40 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8864 (m-80) outliers start: 73 outliers final: 45 residues processed: 280 average time/residue: 0.3726 time to fit residues: 165.6508 Evaluate side-chains 270 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 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 L residue 59 LEU 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 55 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 518 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.083061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058031 restraints weight = 99786.176| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.61 r_work: 0.2987 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26356 Z= 0.211 Angle : 0.640 8.373 35731 Z= 0.339 Chirality : 0.043 0.277 3866 Planarity : 0.004 0.109 4570 Dihedral : 13.584 167.813 4057 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 16.48 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3062 helix: 1.15 (0.16), residues: 1189 sheet: -0.64 (0.23), residues: 518 loop : -1.93 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 77 HIS 0.007 0.001 HIS F 187 PHE 0.029 0.002 PHE H 111 TYR 0.018 0.002 TYR J 106 ARG 0.006 0.000 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 1028) hydrogen bonds : angle 5.11543 ( 3009) covalent geometry : bond 0.00466 (26356) covalent geometry : angle 0.63960 (35731) *********************** 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 305 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 228 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8220 (tt) REVERT: C 90 GLU cc_start: 0.9692 (tm-30) cc_final: 0.9481 (tm-30) REVERT: C 102 MET cc_start: 0.8715 (mmt) cc_final: 0.8467 (mmm) REVERT: C 103 CYS cc_start: 0.9261 (m) cc_final: 0.8832 (p) REVERT: C 167 MET cc_start: 0.8899 (mmm) cc_final: 0.8624 (mmm) REVERT: D 141 MET cc_start: 0.8855 (mtt) cc_final: 0.8308 (pmm) REVERT: D 150 MET cc_start: 0.9098 (tpt) cc_final: 0.8826 (tpp) REVERT: D 271 LYS cc_start: 0.9550 (tppt) cc_final: 0.9296 (tppt) REVERT: D 276 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8727 (p) REVERT: E 167 MET cc_start: 0.7860 (mmm) cc_final: 0.7578 (mmm) REVERT: E 221 MET cc_start: 0.8465 (mtm) cc_final: 0.8171 (mtm) REVERT: F 116 MET cc_start: 0.9436 (mpp) cc_final: 0.8390 (mpp) REVERT: F 209 MET cc_start: 0.8264 (ttp) cc_final: 0.7782 (tmm) REVERT: G 116 MET cc_start: 0.8745 (mpp) cc_final: 0.7972 (mpp) REVERT: G 178 TYR cc_start: 0.8873 (m-80) cc_final: 0.8487 (m-80) REVERT: H 89 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7064 (t80) REVERT: I 38 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.7952 (t70) REVERT: I 39 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8271 (ttm170) REVERT: I 40 TYR cc_start: 0.8688 (m-10) cc_final: 0.8271 (m-10) REVERT: I 41 PHE cc_start: 0.9110 (t80) cc_final: 0.8831 (t80) REVERT: I 55 LEU cc_start: 0.9440 (mt) cc_final: 0.9239 (mt) REVERT: I 65 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8661 (ptmm) REVERT: I 88 ARG cc_start: 0.8782 (tmm-80) cc_final: 0.8438 (tmm-80) REVERT: J 57 ARG cc_start: 0.9217 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: J 68 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: M 31 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6985 (mtt-85) REVERT: N 52 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7805 (mm) REVERT: N 81 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8583 (mm) REVERT: K 300 HIS cc_start: 0.8713 (m90) cc_final: 0.8324 (m-70) REVERT: K 325 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7786 (t80) REVERT: L 40 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8887 (m-80) REVERT: L 56 MET cc_start: 0.8441 (mmp) cc_final: 0.7886 (ttt) outliers start: 77 outliers final: 49 residues processed: 291 average time/residue: 0.3699 time to fit residues: 171.0493 Evaluate side-chains 273 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 3 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 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 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU 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 168 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN E 28 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 518 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.083633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058347 restraints weight = 100656.742| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.68 r_work: 0.2982 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26356 Z= 0.212 Angle : 0.638 8.824 35731 Z= 0.339 Chirality : 0.043 0.277 3866 Planarity : 0.004 0.082 4570 Dihedral : 13.539 167.809 4057 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.79 % Allowed : 17.42 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3062 helix: 1.18 (0.16), residues: 1184 sheet: -0.68 (0.22), residues: 536 loop : -1.91 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 77 HIS 0.007 0.001 HIS F 187 PHE 0.031 0.002 PHE H 111 TYR 0.018 0.002 TYR J 106 ARG 0.007 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 1028) hydrogen bonds : angle 5.10930 ( 3009) covalent geometry : bond 0.00468 (26356) covalent geometry : angle 0.63845 (35731) *********************** 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 297 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8232 (tt) REVERT: C 81 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8185 (t-90) REVERT: C 102 MET cc_start: 0.8725 (mmt) cc_final: 0.8473 (mmm) REVERT: C 103 CYS cc_start: 0.9267 (m) cc_final: 0.8840 (p) REVERT: C 167 MET cc_start: 0.9044 (mmm) cc_final: 0.8656 (mmm) REVERT: D 150 MET cc_start: 0.9062 (tpt) cc_final: 0.8774 (tpp) REVERT: D 271 LYS cc_start: 0.9548 (tppt) cc_final: 0.9261 (tppt) REVERT: D 276 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8724 (p) REVERT: E 167 MET cc_start: 0.7711 (mmm) cc_final: 0.7393 (mmm) REVERT: E 221 MET cc_start: 0.8452 (mtm) cc_final: 0.8214 (mtm) REVERT: F 116 MET cc_start: 0.9433 (mpp) cc_final: 0.8395 (mpp) REVERT: G 116 MET cc_start: 0.8766 (mpp) cc_final: 0.7981 (mpp) REVERT: G 178 TYR cc_start: 0.8896 (m-80) cc_final: 0.8493 (m-80) REVERT: H 87 GLN cc_start: 0.8030 (pp30) cc_final: 0.7713 (pp30) REVERT: H 89 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7210 (t80) REVERT: I 38 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.7950 (t0) REVERT: I 39 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8401 (ttp-170) REVERT: I 41 PHE cc_start: 0.9115 (t80) cc_final: 0.8806 (t80) REVERT: I 55 LEU cc_start: 0.9495 (mt) cc_final: 0.9255 (mt) REVERT: I 65 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8637 (ptmm) REVERT: I 88 ARG cc_start: 0.8772 (tmm-80) cc_final: 0.8493 (tmm-80) REVERT: J 57 ARG cc_start: 0.9182 (mtp85) cc_final: 0.8299 (mtt-85) REVERT: J 68 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: M 31 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7037 (mtt-85) REVERT: N 52 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7774 (mm) REVERT: N 81 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8563 (mm) REVERT: K 300 HIS cc_start: 0.8711 (m90) cc_final: 0.8394 (m-70) REVERT: K 325 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7753 (t80) REVERT: L 40 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: L 56 MET cc_start: 0.8479 (mmp) cc_final: 0.7782 (ttt) outliers start: 74 outliers final: 53 residues processed: 282 average time/residue: 0.3742 time to fit residues: 168.0142 Evaluate side-chains 279 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 214 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 61 HIS Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 240 PHE 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 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 305 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN E 28 ASN F 16 GLN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 ASN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 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 = 0.3742 r_free = 0.3742 target = 0.081275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056598 restraints weight = 105307.756| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.65 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26356 Z= 0.138 Angle : 0.604 10.723 35731 Z= 0.314 Chirality : 0.042 0.236 3866 Planarity : 0.004 0.044 4570 Dihedral : 13.378 164.985 4057 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.79 % Allowed : 17.80 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3062 helix: 1.32 (0.16), residues: 1182 sheet: -0.40 (0.23), residues: 498 loop : -1.85 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 203 HIS 0.006 0.001 HIS H 92 PHE 0.028 0.001 PHE H 111 TYR 0.013 0.001 TYR J 106 ARG 0.006 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1028) hydrogen bonds : angle 4.81345 ( 3009) covalent geometry : bond 0.00306 (26356) covalent geometry : angle 0.60394 (35731) *********************** 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 309 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 235 time to evaluate : 2.948 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: B 209 MET cc_start: 0.8485 (tmm) cc_final: 0.6891 (tmm) REVERT: C 46 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7932 (tt) REVERT: C 81 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.8100 (t-90) REVERT: C 102 MET cc_start: 0.8546 (mmt) cc_final: 0.8277 (mmm) REVERT: C 103 CYS cc_start: 0.8687 (m) cc_final: 0.8320 (m) REVERT: C 167 MET cc_start: 0.9012 (mmm) cc_final: 0.8612 (mmm) REVERT: D 150 MET cc_start: 0.8845 (tpt) cc_final: 0.8542 (tpp) REVERT: D 271 LYS cc_start: 0.9549 (tppt) cc_final: 0.9235 (tppt) REVERT: D 276 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8639 (p) REVERT: E 72 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7199 (pt) REVERT: E 167 MET cc_start: 0.7302 (mmm) cc_final: 0.6978 (mmm) REVERT: E 221 MET cc_start: 0.8412 (mtm) cc_final: 0.8163 (mtm) REVERT: F 116 MET cc_start: 0.9503 (mpp) cc_final: 0.8701 (mpp) REVERT: F 209 MET cc_start: 0.8278 (tmm) cc_final: 0.7570 (ttp) REVERT: G 116 MET cc_start: 0.9042 (mpp) cc_final: 0.8451 (mpp) REVERT: G 178 TYR cc_start: 0.8866 (m-80) cc_final: 0.8536 (m-80) REVERT: H 89 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7259 (t80) REVERT: H 124 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: I 38 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.7991 (t70) REVERT: I 39 ARG cc_start: 0.8990 (mtp180) cc_final: 0.8463 (ttp-170) REVERT: I 40 TYR cc_start: 0.8689 (m-10) cc_final: 0.8358 (m-10) REVERT: I 41 PHE cc_start: 0.9148 (t80) cc_final: 0.8862 (t80) REVERT: I 55 LEU cc_start: 0.9448 (mt) cc_final: 0.9232 (mt) REVERT: I 65 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8718 (ptmm) REVERT: I 88 ARG cc_start: 0.8726 (tmm-80) cc_final: 0.8449 (tmm-80) REVERT: J 27 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8782 (mm-30) REVERT: J 57 ARG cc_start: 0.9154 (mtp85) cc_final: 0.8331 (mtt-85) REVERT: J 68 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: M 31 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: N 171 MET cc_start: 0.8440 (tpt) cc_final: 0.8198 (mmm) REVERT: K 300 HIS cc_start: 0.8499 (m90) cc_final: 0.7872 (m-70) REVERT: K 325 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7645 (t80) REVERT: L 40 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: L 56 MET cc_start: 0.8440 (mmp) cc_final: 0.7854 (ttt) outliers start: 74 outliers final: 49 residues processed: 294 average time/residue: 0.3666 time to fit residues: 171.9192 Evaluate side-chains 283 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 HIS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 222 ASN Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 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 60 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 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 570 PHE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain A residue 38 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 165 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 85 HIS M 130 GLN N 103 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.083146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058391 restraints weight = 104778.054| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.80 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26356 Z= 0.109 Angle : 0.600 14.033 35731 Z= 0.308 Chirality : 0.041 0.201 3866 Planarity : 0.004 0.046 4570 Dihedral : 13.229 162.516 4057 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.15 % Allowed : 18.48 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3062 helix: 1.41 (0.16), residues: 1181 sheet: -0.33 (0.23), residues: 536 loop : -1.78 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 203 HIS 0.007 0.001 HIS H 92 PHE 0.030 0.001 PHE H 111 TYR 0.013 0.001 TYR H 106 ARG 0.004 0.000 ARG H 57 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1028) hydrogen bonds : angle 4.58323 ( 3009) covalent geometry : bond 0.00236 (26356) covalent geometry : angle 0.60031 (35731) *********************** 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 305 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 2.790 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: 0.8352 (tmm) cc_final: 0.6795 (tmm) REVERT: C 46 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7866 (tt) REVERT: C 102 MET cc_start: 0.8447 (mmt) cc_final: 0.7802 (mmm) REVERT: C 103 CYS cc_start: 0.8636 (m) cc_final: 0.8254 (m) REVERT: C 167 MET cc_start: 0.8956 (mmm) cc_final: 0.8530 (mmm) REVERT: D 17 ASP cc_start: 0.8517 (m-30) cc_final: 0.8230 (m-30) REVERT: D 35 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8434 (tm-30) REVERT: D 150 MET cc_start: 0.8742 (tpt) cc_final: 0.8405 (tpp) REVERT: D 271 LYS cc_start: 0.9602 (tppt) cc_final: 0.9307 (tppt) REVERT: E 167 MET cc_start: 0.6926 (mmm) cc_final: 0.6599 (mmm) REVERT: E 221 MET cc_start: 0.8569 (mtm) cc_final: 0.8367 (mtm) REVERT: F 116 MET cc_start: 0.9539 (mpp) cc_final: 0.8818 (mpp) REVERT: F 178 TYR cc_start: 0.9030 (m-80) cc_final: 0.8499 (m-80) REVERT: F 209 MET cc_start: 0.8734 (tmm) cc_final: 0.7929 (ttp) REVERT: G 116 MET cc_start: 0.9083 (mpp) cc_final: 0.8473 (mpp) REVERT: G 178 TYR cc_start: 0.8798 (m-80) cc_final: 0.8288 (m-80) REVERT: G 209 MET cc_start: 0.3598 (mmm) cc_final: 0.3378 (mmm) REVERT: H 22 GLU cc_start: 0.9060 (pt0) cc_final: 0.8746 (pt0) REVERT: H 77 TRP cc_start: 0.7667 (t60) cc_final: 0.7304 (t60) REVERT: H 89 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7570 (t80) REVERT: H 124 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8920 (pm20) REVERT: I 38 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7963 (t70) REVERT: I 39 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8419 (ttp-170) REVERT: I 40 TYR cc_start: 0.8601 (m-10) cc_final: 0.8282 (m-10) REVERT: I 41 PHE cc_start: 0.9115 (t80) cc_final: 0.8772 (t80) REVERT: I 52 PHE cc_start: 0.9038 (m-80) cc_final: 0.8205 (m-80) REVERT: I 65 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8726 (ptmm) REVERT: I 88 ARG cc_start: 0.8739 (tmm-80) cc_final: 0.8482 (tmm-80) REVERT: J 27 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8730 (mm-30) REVERT: J 41 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: J 57 ARG cc_start: 0.9181 (mtp85) cc_final: 0.8478 (mtt-85) REVERT: J 68 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: M 31 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6947 (mtt-85) REVERT: N 165 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6937 (p) REVERT: N 171 MET cc_start: 0.7905 (tpt) cc_final: 0.7697 (mmm) REVERT: N 195 CYS cc_start: 0.9415 (t) cc_final: 0.9075 (p) REVERT: K 300 HIS cc_start: 0.8493 (m90) cc_final: 0.8147 (m-70) REVERT: K 325 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7585 (t80) REVERT: L 40 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: L 56 MET cc_start: 0.8365 (mmp) cc_final: 0.7864 (ttt) outliers start: 57 outliers final: 31 residues processed: 293 average time/residue: 0.3693 time to fit residues: 170.4689 Evaluate side-chains 272 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 86 VAL 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 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 41 PHE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 325 PHE Chi-restraints excluded: chain K residue 426 GLU 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 L residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 84 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 185 optimal weight: 0.0470 chunk 297 optimal weight: 40.0000 chunk 300 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** K 8 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.080644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055854 restraints weight = 106108.697| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.69 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26356 Z= 0.198 Angle : 0.664 14.479 35731 Z= 0.342 Chirality : 0.043 0.259 3866 Planarity : 0.004 0.044 4570 Dihedral : 13.305 166.994 4057 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.96 % Allowed : 18.97 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3062 helix: 1.36 (0.16), residues: 1181 sheet: -0.49 (0.23), residues: 536 loop : -1.70 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 203 HIS 0.007 0.001 HIS H 62 PHE 0.034 0.002 PHE M 66 TYR 0.012 0.002 TYR D 7 ARG 0.008 0.000 ARG G 224 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 1028) hydrogen bonds : angle 4.85803 ( 3009) covalent geometry : bond 0.00442 (26356) covalent geometry : angle 0.66353 (35731) ********************** 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 277 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 2.909 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: 0.8555 (tmm) cc_final: 0.6985 (tmm) REVERT: C 46 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8079 (tt) REVERT: C 102 MET cc_start: 0.8656 (mmt) cc_final: 0.8420 (mmm) REVERT: C 103 CYS cc_start: 0.8661 (m) cc_final: 0.8308 (m) REVERT: C 167 MET cc_start: 0.9041 (mmm) cc_final: 0.8649 (mmm) REVERT: D 17 ASP cc_start: 0.8430 (m-30) cc_final: 0.8159 (m-30) REVERT: D 150 MET cc_start: 0.8957 (tpt) cc_final: 0.8668 (tpp) REVERT: D 271 LYS cc_start: 0.9609 (tppt) cc_final: 0.9293 (tppt) REVERT: E 167 MET cc_start: 0.7275 (mmm) cc_final: 0.6941 (mmm) REVERT: E 221 MET cc_start: 0.8470 (mtm) cc_final: 0.8236 (mtm) REVERT: F 116 MET cc_start: 0.9384 (mpp) cc_final: 0.8523 (mpp) REVERT: F 178 TYR cc_start: 0.8963 (m-80) cc_final: 0.8460 (m-80) REVERT: F 209 MET cc_start: 0.8540 (tmm) cc_final: 0.7887 (ttp) REVERT: G 116 MET cc_start: 0.9094 (mpp) cc_final: 0.8454 (mpp) REVERT: G 178 TYR cc_start: 0.8801 (m-80) cc_final: 0.8437 (m-80) REVERT: G 209 MET cc_start: 0.4007 (mmm) cc_final: 0.3747 (mmm) REVERT: G 214 HIS cc_start: 0.7856 (p-80) cc_final: 0.7070 (m-70) REVERT: H 71 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8247 (mmm160) REVERT: H 77 TRP cc_start: 0.7722 (t60) cc_final: 0.7377 (t60) REVERT: H 89 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7587 (t80) REVERT: I 38 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8173 (t70) REVERT: I 39 ARG cc_start: 0.8937 (mtp180) cc_final: 0.8623 (mtp180) REVERT: I 40 TYR cc_start: 0.8617 (m-10) cc_final: 0.8342 (m-10) REVERT: I 41 PHE cc_start: 0.9185 (t80) cc_final: 0.8881 (t80) REVERT: I 65 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8704 (ptmm) REVERT: I 88 ARG cc_start: 0.8801 (tmm-80) cc_final: 0.8510 (tmm-80) REVERT: J 27 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8832 (mm-30) REVERT: J 41 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: J 57 ARG cc_start: 0.9269 (mtp85) cc_final: 0.8581 (mtt-85) REVERT: J 68 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: M 31 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6966 (mtt-85) REVERT: N 171 MET cc_start: 0.8065 (tpt) cc_final: 0.7846 (mmm) REVERT: N 195 CYS cc_start: 0.9436 (t) cc_final: 0.9126 (p) REVERT: K 300 HIS cc_start: 0.8539 (m90) cc_final: 0.8082 (m-70) REVERT: L 40 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: L 56 MET cc_start: 0.8555 (mmp) cc_final: 0.7931 (ttt) outliers start: 52 outliers final: 41 residues processed: 267 average time/residue: 0.3738 time to fit residues: 158.5878 Evaluate side-chains 270 residues out of total 2654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL 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 46 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 86 VAL 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 228 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 92 HIS Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain J residue 41 PHE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 268 VAL Chi-restraints excluded: chain M residue 276 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 139 TYR Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain K residue 250 TYR Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 312 TYR Chi-restraints excluded: chain K residue 426 GLU 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 L residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 299 optimal weight: 20.0000 chunk 302 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 277 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056730 restraints weight = 105426.278| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 4.74 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26356 Z= 0.141 Angle : 0.630 14.866 35731 Z= 0.323 Chirality : 0.042 0.233 3866 Planarity : 0.004 0.046 4570 Dihedral : 13.269 165.326 4057 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.38 % Allowed : 18.67 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3062 helix: 1.39 (0.16), residues: 1182 sheet: -0.42 (0.23), residues: 533 loop : -1.71 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 203 HIS 0.006 0.001 HIS H 62 PHE 0.032 0.001 PHE H 111 TYR 0.018 0.001 TYR A 24 ARG 0.007 0.000 ARG H 57 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 1028) hydrogen bonds : angle 4.70974 ( 3009) covalent geometry : bond 0.00316 (26356) covalent geometry : angle 0.62972 (35731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14162.62 seconds wall clock time: 243 minutes 39.53 seconds (14619.53 seconds total)