Starting phenix.real_space_refine on Thu Mar 5 16:51:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfo_27409/03_2026/8dfo_27409.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 45 5.49 5 S 135 5.16 5 C 14839 2.51 5 N 4259 2.21 5 O 4583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23861 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1774 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2112 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3261 Classifications: {'peptide': 415} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 388} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 960 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 17, 'rna3p': 27} Chain: "M" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 466 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 5.65, per 1000 atoms: 0.24 Number of scatterers: 23861 At special positions: 0 Unit cell: (119.38, 117.5, 202.1, 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 135 16.00 P 45 15.00 O 4583 8.00 N 4259 7.00 C 14839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 807.1 milliseconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 36 sheets defined 38.0% alpha, 23.7% beta 0 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.784A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.167A pdb=" N ASP A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.883A pdb=" N ASN B 112 " --> pdb=" O TRP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.561A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.545A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.548A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.567A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.320A pdb=" N HIS C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.628A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.606A pdb=" N THR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.539A pdb=" N LYS D 199 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.785A pdb=" N SER D 263 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.540A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.930A pdb=" N LYS E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.551A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.595A pdb=" N LYS F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.916A pdb=" N GLY G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.645A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 98 through 113 Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.560A pdb=" N LYS G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.163A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 255 removed outlier: 3.607A pdb=" N LEU G 254 " --> pdb=" O LYS G 250 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.787A pdb=" N GLY H 28 " --> pdb=" O PRO H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 removed outlier: 3.763A pdb=" N LEU H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 removed outlier: 4.177A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 247 through 255 removed outlier: 3.583A pdb=" N ASP H 253 " --> pdb=" O HIS H 249 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 255 " --> pdb=" O LEU H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 4 through 14 Processing helix chain 'I' and resid 239 through 255 removed outlier: 3.568A pdb=" N VAL I 247 " --> pdb=" O ALA I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 287 removed outlier: 4.343A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 287 " --> pdb=" O PHE I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 373 through 389 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 420 through 427 Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 455 through 459 removed outlier: 4.018A pdb=" N ASP I 458 " --> pdb=" O ARG I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 482 Processing helix chain 'I' and resid 497 through 517 Processing helix chain 'I' and resid 523 through 528 removed outlier: 3.758A pdb=" N ARG I 527 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 535 through 557 removed outlier: 3.885A pdb=" N VAL I 539 " --> pdb=" O ASN I 535 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS I 541 " --> pdb=" O GLY I 537 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 556 " --> pdb=" O ALA I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 576 removed outlier: 3.825A pdb=" N GLU I 568 " --> pdb=" O ALA I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 603 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 47 through 69 removed outlier: 3.655A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.843A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 3.516A pdb=" N ARG K 39 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.708A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 73 No H-bonds generated for 'chain 'K' and resid 73 through 73' Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 9 through 18 Processing helix chain 'M' and resid 42 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.769A pdb=" N ARG A 31 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU A 115 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 116 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 19 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.552A pdb=" N ARG A 75 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 196 removed outlier: 5.697A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.867A pdb=" N THR B 174 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 3.506A pdb=" N GLY B 184 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.921A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 124 removed outlier: 4.515A pdb=" N GLY C 130 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.753A pdb=" N TYR D 183 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU D 17 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 185 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP D 15 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 187 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 13 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS D 189 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 11 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE D 191 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU D 9 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 234 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AB9, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 138 removed outlier: 6.880A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 42 removed outlier: 3.643A pdb=" N THR F 174 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.832A pdb=" N ARG F 7 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.557A pdb=" N GLY F 130 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 42 removed outlier: 5.134A pdb=" N GLY G 40 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 185 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR G 183 " --> pdb=" O PRO G 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 138 removed outlier: 5.939A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU G 17 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET G 229 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.737A pdb=" N GLY G 130 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.585A pdb=" N LYS H 233 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP H 15 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER H 231 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU H 17 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET H 229 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AD5, first strand: chain 'H' and resid 257 through 259 Processing sheet with id=AD6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD8, first strand: chain 'I' and resid 262 through 264 removed outlier: 6.630A pdb=" N VAL I 354 " --> pdb=" O TRP I 369 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP I 369 " --> pdb=" O VAL I 354 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY I 356 " --> pdb=" O ARG I 367 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 22 through 24 1005 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.43: 10772 1.43 - 1.82: 13669 1.82 - 2.21: 0 2.21 - 2.61: 0 2.61 - 3.00: 2 Bond restraints: 24443 Sorted by residual: bond pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 1.332 2.998 -1.665 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " ideal model delta sigma weight residual 1.492 2.673 -1.181 5.00e-02 4.00e+02 5.58e+02 bond pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 1.503 1.038 0.465 3.40e-02 8.65e+02 1.87e+02 bond pdb=" CE1 HIS C 249 " pdb=" NE2 HIS C 249 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.02e+01 bond pdb=" CE1 HIS C 54 " pdb=" NE2 HIS C 54 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.90e+01 ... (remaining 24438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 33265 21.21 - 42.42: 3 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 2 Bond angle restraints: 33270 Sorted by residual: angle pdb=" O LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 122.59 37.08 85.51 1.33e+00 5.65e-01 4.13e+03 angle pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 116.84 84.80 32.04 1.71e+00 3.42e-01 3.51e+02 angle pdb=" CA PRO H 92 " pdb=" N PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 112.00 89.53 22.47 1.40e+00 5.10e-01 2.58e+02 angle pdb=" N PRO H 92 " pdb=" CA PRO H 92 " pdb=" CB PRO H 92 " ideal model delta sigma weight residual 103.19 92.31 10.88 1.00e+00 1.00e+00 1.18e+02 ... (remaining 33265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 14362 35.53 - 71.07: 523 71.07 - 106.60: 50 106.60 - 142.14: 7 142.14 - 177.67: 14 Dihedral angle restraints: 14956 sinusoidal: 6527 harmonic: 8429 Sorted by residual: dihedral pdb=" C5' U L 5 " pdb=" C4' U L 5 " pdb=" C3' U L 5 " pdb=" O3' U L 5 " ideal model delta sinusoidal sigma weight residual 147.00 74.29 72.71 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C L 18 " pdb=" C3' C L 18 " pdb=" C2' C L 18 " pdb=" C1' C L 18 " ideal model delta sinusoidal sigma weight residual -35.00 36.08 -71.08 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' G L 31 " pdb=" C3' G L 31 " pdb=" C2' G L 31 " pdb=" C1' G L 31 " ideal model delta sinusoidal sigma weight residual -35.00 35.81 -70.81 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 14953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3302 0.148 - 0.296: 73 0.296 - 0.444: 84 0.444 - 0.592: 171 0.592 - 0.740: 64 Chirality restraints: 3694 Sorted by residual: chirality pdb=" CG LEU I 364 " pdb=" CB LEU I 364 " pdb=" CD1 LEU I 364 " pdb=" CD2 LEU I 364 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CG LEU C 12 " pdb=" CB LEU C 12 " pdb=" CD1 LEU C 12 " pdb=" CD2 LEU C 12 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB VAL C 11 " pdb=" CA VAL C 11 " pdb=" CG1 VAL C 11 " pdb=" CG2 VAL C 11 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 3691 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U L 6 " -0.179 2.00e-02 2.50e+03 8.31e-02 1.55e+02 pdb=" N1 U L 6 " 0.078 2.00e-02 2.50e+03 pdb=" C2 U L 6 " 0.033 2.00e-02 2.50e+03 pdb=" O2 U L 6 " 0.046 2.00e-02 2.50e+03 pdb=" N3 U L 6 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U L 6 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U L 6 " -0.102 2.00e-02 2.50e+03 pdb=" C5 U L 6 " 0.039 2.00e-02 2.50e+03 pdb=" C6 U L 6 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G L 7 " 0.118 2.00e-02 2.50e+03 5.10e-02 7.82e+01 pdb=" N9 G L 7 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G L 7 " -0.064 2.00e-02 2.50e+03 pdb=" N7 G L 7 " -0.050 2.00e-02 2.50e+03 pdb=" C5 G L 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G L 7 " 0.029 2.00e-02 2.50e+03 pdb=" O6 G L 7 " 0.045 2.00e-02 2.50e+03 pdb=" N1 G L 7 " 0.052 2.00e-02 2.50e+03 pdb=" C2 G L 7 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G L 7 " -0.051 2.00e-02 2.50e+03 pdb=" N3 G L 7 " -0.044 2.00e-02 2.50e+03 pdb=" C4 G L 7 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 8 " -0.077 2.00e-02 2.50e+03 3.95e-02 3.13e+01 pdb=" CG TYR C 8 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 8 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR C 8 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 8 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR C 8 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 8 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 8 " -0.049 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 75 2.36 - 2.99: 13234 2.99 - 3.63: 34940 3.63 - 4.26: 55886 4.26 - 4.90: 95992 Nonbonded interactions: 200127 Sorted by model distance: nonbonded pdb=" O2' G L 12 " pdb=" O5' C L 13 " model vdw 1.724 3.040 nonbonded pdb=" O2' A L 15 " pdb=" O5' U L 16 " model vdw 1.742 3.040 nonbonded pdb=" O2' U L 42 " pdb=" O5' C L 43 " model vdw 1.797 3.040 nonbonded pdb=" O2' G L 33 " pdb=" O5' C L 34 " model vdw 1.802 3.040 nonbonded pdb=" O2' C L 34 " pdb=" OP1 G L 35 " model vdw 1.839 3.040 ... (remaining 200122 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' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=0.98 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: 4.480 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.440 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0735 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 : 0.022 1.665 24443 Z= 1.194 Angle : 1.638 106.046 33270 Z= 0.977 Chirality : 0.163 0.740 3694 Planarity : 0.006 0.100 4206 Dihedral : 18.530 177.673 9498 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 0.57 % Allowed : 11.72 % Favored : 87.71 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2860 helix: 0.78 (0.17), residues: 916 sheet: -0.09 (0.22), residues: 559 loop : -1.10 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 363 TYR 0.077 0.003 TYR C 8 PHE 0.054 0.003 PHE I 225 TRP 0.036 0.003 TRP C 211 HIS 0.017 0.001 HIS I 198 Details of bonding type rmsd covalent geometry : bond 0.02152 (24443) covalent geometry : angle 1.63834 (33270) hydrogen bonds : bond 0.18960 ( 1001) hydrogen bonds : angle 8.21135 ( 2841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 0.880 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 175 MET cc_start: 0.2011 (tpp) cc_final: 0.1507 (ptt) REVERT: D 183 TYR cc_start: 0.1513 (t80) cc_final: 0.0784 (t80) REVERT: E 138 MET cc_start: 0.2902 (mtt) cc_final: 0.0632 (mpp) REVERT: G 175 MET cc_start: 0.5701 (tmm) cc_final: 0.5314 (tmm) REVERT: H 251 LEU cc_start: -0.0135 (mt) cc_final: -0.0392 (mt) REVERT: I 343 MET cc_start: -0.2998 (mtp) cc_final: -0.4121 (tpt) REVERT: I 526 ASP cc_start: 0.2245 (m-30) cc_final: 0.2023 (m-30) REVERT: K 78 HIS cc_start: 0.4984 (t70) cc_final: 0.4746 (t-170) REVERT: M 1 MET cc_start: 0.3480 (mtt) cc_final: 0.2898 (ttp) outliers start: 14 outliers final: 2 residues processed: 347 average time/residue: 0.1781 time to fit residues: 93.4813 Evaluate side-chains 219 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain I residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN C 76 ASN D 150 GLN D 179 HIS ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS H 216 ASN I 198 HIS J 111 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.303958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.287994 restraints weight = 44162.961| |-----------------------------------------------------------------------------| r_work (start): 0.5127 rms_B_bonded: 2.75 r_work: 0.5056 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.5056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1093 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24443 Z= 0.145 Angle : 0.703 13.103 33270 Z= 0.368 Chirality : 0.048 0.509 3694 Planarity : 0.005 0.067 4206 Dihedral : 15.335 168.665 3894 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 2.09 % Allowed : 12.49 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2862 helix: 1.38 (0.17), residues: 951 sheet: 0.37 (0.22), residues: 539 loop : -0.72 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 104 TYR 0.025 0.002 TYR I 10 PHE 0.033 0.002 PHE K 18 TRP 0.018 0.002 TRP M 31 HIS 0.007 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00303 (24443) covalent geometry : angle 0.70280 (33270) hydrogen bonds : bond 0.03703 ( 1001) hydrogen bonds : angle 5.56892 ( 2841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.855 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 175 MET cc_start: 0.3504 (pmm) cc_final: 0.2031 (ptp) REVERT: C 30 MET cc_start: 0.0604 (mtp) cc_final: -0.0224 (mtp) REVERT: C 109 MET cc_start: 0.1923 (ppp) cc_final: -0.0523 (mtt) REVERT: C 123 MET cc_start: -0.2277 (ptp) cc_final: -0.4158 (mtm) REVERT: C 138 MET cc_start: 0.4017 (ppp) cc_final: 0.0026 (mtm) REVERT: C 175 MET cc_start: 0.2571 (tpp) cc_final: 0.2048 (mtm) REVERT: D 128 ASN cc_start: 0.1483 (t0) cc_final: 0.0850 (t0) REVERT: D 183 TYR cc_start: 0.2583 (t80) cc_final: 0.1541 (t80) REVERT: E 114 TYR cc_start: 0.4489 (t80) cc_final: 0.3988 (t80) REVERT: E 138 MET cc_start: 0.3076 (mtt) cc_final: 0.1214 (mpp) REVERT: F 1 MET cc_start: -0.0574 (ptm) cc_final: -0.2041 (mtp) REVERT: I 343 MET cc_start: -0.2765 (mtp) cc_final: -0.4391 (tpt) REVERT: I 346 MET cc_start: -0.0880 (OUTLIER) cc_final: -0.2023 (mmm) REVERT: K 97 MET cc_start: -0.0722 (mmp) cc_final: -0.3397 (mmt) REVERT: M 1 MET cc_start: 0.3483 (mtt) cc_final: 0.2751 (ttp) outliers start: 51 outliers final: 20 residues processed: 282 average time/residue: 0.1636 time to fit residues: 71.9949 Evaluate side-chains 236 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 353 HIS Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 140 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 70 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN D 70 GLN E 220 HIS E 245 ASN G 249 HIS H 79 HIS I 183 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 535 ASN I 538 GLN J 33 ASN K 47 ASN M 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.303510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.290187 restraints weight = 43862.857| |-----------------------------------------------------------------------------| r_work (start): 0.5154 rms_B_bonded: 2.52 r_work: 0.5091 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.5091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2139 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24443 Z= 0.191 Angle : 0.783 12.857 33270 Z= 0.403 Chirality : 0.049 0.348 3694 Planarity : 0.006 0.068 4206 Dihedral : 14.861 171.712 3891 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 2.70 % Allowed : 13.56 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 2862 helix: 0.99 (0.16), residues: 955 sheet: 0.41 (0.22), residues: 539 loop : -0.76 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 156 TYR 0.022 0.003 TYR A 34 PHE 0.025 0.003 PHE I 352 TRP 0.022 0.003 TRP M 40 HIS 0.013 0.002 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00409 (24443) covalent geometry : angle 0.78285 (33270) hydrogen bonds : bond 0.04296 ( 1001) hydrogen bonds : angle 5.60935 ( 2841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 249 time to evaluate : 0.837 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: A 27 MET cc_start: 0.5322 (mmm) cc_final: 0.3835 (mmm) REVERT: A 113 THR cc_start: 0.4448 (m) cc_final: 0.4175 (m) REVERT: B 1 MET cc_start: 0.2371 (tmm) cc_final: 0.0621 (ppp) REVERT: B 140 PHE cc_start: 0.6682 (m-10) cc_final: 0.6318 (m-10) REVERT: C 30 MET cc_start: 0.2100 (mtp) cc_final: -0.0081 (mtp) REVERT: C 123 MET cc_start: -0.1750 (ptp) cc_final: -0.3132 (mtm) REVERT: C 138 MET cc_start: 0.4631 (ppp) cc_final: 0.2575 (ppp) REVERT: D 67 ILE cc_start: 0.4191 (OUTLIER) cc_final: 0.3919 (tt) REVERT: E 114 TYR cc_start: 0.3819 (t80) cc_final: 0.3446 (t80) REVERT: E 138 MET cc_start: 0.3533 (mtt) cc_final: 0.2834 (mtm) REVERT: F 157 MET cc_start: 0.2042 (ptp) cc_final: 0.1786 (ptp) REVERT: G 138 MET cc_start: -0.0371 (mpp) cc_final: -0.2271 (ptm) REVERT: H 217 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.5017 (ptt) REVERT: I 326 MET cc_start: 0.2078 (tpt) cc_final: -0.0339 (ptp) REVERT: I 343 MET cc_start: -0.2968 (mtp) cc_final: -0.4195 (tpt) REVERT: I 346 MET cc_start: -0.1166 (OUTLIER) cc_final: -0.2299 (tpt) REVERT: I 448 ARG cc_start: 0.2907 (OUTLIER) cc_final: 0.1342 (tpp-160) REVERT: I 514 GLU cc_start: 0.1641 (pt0) cc_final: 0.0996 (tt0) REVERT: I 542 MET cc_start: 0.1070 (ptp) cc_final: 0.0822 (ppp) REVERT: I 585 MET cc_start: -0.4017 (mtp) cc_final: -0.4220 (mtp) REVERT: J 86 ILE cc_start: 0.4292 (mt) cc_final: 0.4055 (mt) REVERT: K 97 MET cc_start: -0.0429 (mmp) cc_final: -0.1980 (mtm) outliers start: 66 outliers final: 26 residues processed: 296 average time/residue: 0.1604 time to fit residues: 74.7822 Evaluate side-chains 232 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 448 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 109 TYR Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 105 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN D 189 HIS E 216 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN I 221 ASN I 222 ASN I 327 HIS ** I 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.303196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5157 r_free = 0.5157 target = 0.289596 restraints weight = 43438.293| |-----------------------------------------------------------------------------| r_work (start): 0.5148 rms_B_bonded: 2.55 r_work: 0.5081 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.5081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2360 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24443 Z= 0.138 Angle : 0.651 11.060 33270 Z= 0.335 Chirality : 0.046 0.286 3694 Planarity : 0.005 0.069 4206 Dihedral : 14.455 178.427 3891 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 2.46 % Allowed : 14.79 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2862 helix: 1.28 (0.16), residues: 965 sheet: 0.29 (0.22), residues: 561 loop : -0.61 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 142 TYR 0.014 0.002 TYR F 68 PHE 0.027 0.002 PHE G 119 TRP 0.016 0.002 TRP M 40 HIS 0.006 0.001 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00296 (24443) covalent geometry : angle 0.65081 (33270) hydrogen bonds : bond 0.03406 ( 1001) hydrogen bonds : angle 5.22467 ( 2841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.3375 (tp40) cc_final: 0.3031 (tp40) REVERT: B 1 MET cc_start: 0.2224 (tmm) cc_final: 0.0727 (ppp) REVERT: C 30 MET cc_start: 0.2769 (mtp) cc_final: 0.0477 (mtp) REVERT: C 123 MET cc_start: -0.2278 (ptp) cc_final: -0.2531 (mtm) REVERT: C 138 MET cc_start: 0.4529 (OUTLIER) cc_final: 0.1892 (ptt) REVERT: E 109 MET cc_start: -0.0757 (mmm) cc_final: -0.1178 (mtm) REVERT: E 114 TYR cc_start: 0.3848 (t80) cc_final: 0.3488 (t80) REVERT: E 138 MET cc_start: 0.3445 (mtt) cc_final: 0.1622 (mpp) REVERT: F 175 MET cc_start: 0.4329 (tmm) cc_final: 0.3075 (ttm) REVERT: F 179 HIS cc_start: 0.4497 (m-70) cc_final: 0.3736 (m170) REVERT: G 138 MET cc_start: -0.0319 (mpp) cc_final: -0.2370 (ptm) REVERT: H 157 MET cc_start: 0.3380 (ttp) cc_final: 0.2458 (mmp) REVERT: H 205 GLU cc_start: 0.5232 (mp0) cc_final: 0.4362 (pt0) REVERT: I 334 ARG cc_start: 0.3654 (ttt180) cc_final: 0.2866 (tmm160) REVERT: I 343 MET cc_start: -0.2630 (mtp) cc_final: -0.4031 (tpt) REVERT: I 346 MET cc_start: -0.1135 (OUTLIER) cc_final: -0.2319 (tpt) REVERT: I 570 MET cc_start: 0.3445 (mtt) cc_final: 0.3164 (mtt) REVERT: I 594 MET cc_start: 0.0404 (mmp) cc_final: 0.0184 (tpp) REVERT: J 82 MET cc_start: 0.1234 (mtm) cc_final: -0.0246 (tmm) REVERT: J 86 ILE cc_start: 0.4223 (mt) cc_final: 0.3591 (mt) REVERT: M 51 GLU cc_start: 0.3855 (OUTLIER) cc_final: 0.3619 (mp0) outliers start: 60 outliers final: 30 residues processed: 283 average time/residue: 0.1497 time to fit residues: 68.6374 Evaluate side-chains 248 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 154 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 179 HIS ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN G 54 HIS G 179 HIS H 39 HIS ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN I 260 GLN I 327 HIS ** I 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 535 ASN I 538 GLN I 546 ASN J 112 GLN K 112 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.291173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.273547 restraints weight = 41274.186| |-----------------------------------------------------------------------------| r_work (start): 0.5019 rms_B_bonded: 2.36 r_work: 0.4955 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3731 moved from start: 1.0249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 24443 Z= 0.340 Angle : 1.111 18.643 33270 Z= 0.586 Chirality : 0.062 0.363 3694 Planarity : 0.008 0.096 4206 Dihedral : 15.589 176.950 3891 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.64 % Favored : 93.26 % Rotamer: Outliers : 3.81 % Allowed : 16.55 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 2862 helix: -0.63 (0.16), residues: 937 sheet: -0.59 (0.24), residues: 477 loop : -1.51 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 222 TYR 0.037 0.004 TYR E 68 PHE 0.033 0.004 PHE E 14 TRP 0.039 0.004 TRP M 40 HIS 0.012 0.003 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00762 (24443) covalent geometry : angle 1.11081 (33270) hydrogen bonds : bond 0.07050 ( 1001) hydrogen bonds : angle 7.61345 ( 2841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 257 time to evaluate : 0.832 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: A 108 GLN cc_start: 0.3721 (tp40) cc_final: 0.3292 (tp40) REVERT: B 1 MET cc_start: 0.1910 (tmm) cc_final: 0.0897 (tmm) REVERT: C 7 ARG cc_start: 0.6930 (ttp-170) cc_final: 0.6198 (ttp-170) REVERT: C 123 MET cc_start: -0.0085 (ptp) cc_final: -0.1908 (mmm) REVERT: C 138 MET cc_start: 0.4454 (OUTLIER) cc_final: 0.3059 (mmt) REVERT: C 273 TYR cc_start: 0.5254 (m-80) cc_final: 0.4703 (m-80) REVERT: C 289 MET cc_start: 0.4394 (pmm) cc_final: 0.2885 (tmm) REVERT: D 41 LEU cc_start: 0.5733 (mt) cc_final: 0.5317 (mp) REVERT: D 145 GLU cc_start: 0.4291 (OUTLIER) cc_final: 0.3855 (tt0) REVERT: D 211 TRP cc_start: 0.0279 (OUTLIER) cc_final: -0.0201 (p-90) REVERT: D 229 MET cc_start: 0.6663 (ptt) cc_final: 0.5925 (ptt) REVERT: D 235 ILE cc_start: -0.2455 (OUTLIER) cc_final: -0.3296 (mp) REVERT: E 109 MET cc_start: -0.1552 (mmm) cc_final: -0.2262 (mtm) REVERT: E 242 ARG cc_start: 0.4253 (ptm160) cc_final: 0.3255 (ttt180) REVERT: F 9 GLU cc_start: 0.0567 (OUTLIER) cc_final: -0.1629 (mm-30) REVERT: F 30 MET cc_start: 0.0761 (tpt) cc_final: 0.0393 (tpt) REVERT: F 191 PHE cc_start: 0.4183 (OUTLIER) cc_final: 0.3163 (m-80) REVERT: F 217 MET cc_start: 0.2567 (mtt) cc_final: 0.1296 (mtm) REVERT: F 241 ASN cc_start: 0.3289 (OUTLIER) cc_final: 0.2246 (m110) REVERT: G 123 MET cc_start: 0.0497 (OUTLIER) cc_final: 0.0106 (ptm) REVERT: G 235 ILE cc_start: -0.0881 (OUTLIER) cc_final: -0.1334 (mm) REVERT: H 39 HIS cc_start: 0.5860 (OUTLIER) cc_final: 0.5546 (m90) REVERT: H 44 ASP cc_start: 0.4687 (p0) cc_final: 0.4451 (t0) REVERT: H 76 ASN cc_start: 0.3512 (m-40) cc_final: 0.2092 (p0) REVERT: H 157 MET cc_start: 0.3609 (ttp) cc_final: 0.2454 (mmp) REVERT: H 205 GLU cc_start: 0.5517 (mp0) cc_final: 0.4652 (pt0) REVERT: I 343 MET cc_start: -0.2650 (mtp) cc_final: -0.3793 (tpt) REVERT: I 346 MET cc_start: -0.1455 (mmt) cc_final: -0.2436 (tpp) REVERT: I 408 ARG cc_start: 0.4425 (OUTLIER) cc_final: 0.2745 (ttm-80) REVERT: I 483 ARG cc_start: 0.4990 (mmp-170) cc_final: 0.3886 (mtp85) REVERT: I 598 TYR cc_start: 0.2923 (OUTLIER) cc_final: 0.1871 (p90) REVERT: J 86 ILE cc_start: 0.4397 (mt) cc_final: 0.4182 (mt) REVERT: K 5 PRO cc_start: 0.8368 (Cg_endo) cc_final: 0.8142 (Cg_exo) REVERT: K 83 MET cc_start: 0.5203 (tpt) cc_final: 0.4811 (tpt) REVERT: M 51 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.4578 (mp0) outliers start: 93 outliers final: 43 residues processed: 336 average time/residue: 0.1492 time to fit residues: 81.3675 Evaluate side-chains 278 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 109 TYR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 129 optimal weight: 0.8980 chunk 175 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 277 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 239 HIS E 245 ASN F 39 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN G 239 HIS I 360 ASN I 535 ASN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5213 r_free = 0.5213 target = 0.296859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5099 r_free = 0.5099 target = 0.280512 restraints weight = 42195.606| |-----------------------------------------------------------------------------| r_work (start): 0.5060 rms_B_bonded: 2.46 r_work: 0.4995 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3484 moved from start: 1.0102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24443 Z= 0.138 Angle : 0.696 16.400 33270 Z= 0.359 Chirality : 0.047 0.257 3694 Planarity : 0.005 0.054 4206 Dihedral : 14.516 179.471 3891 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 2.62 % Allowed : 18.11 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 2862 helix: 0.32 (0.16), residues: 961 sheet: -0.50 (0.23), residues: 507 loop : -1.16 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 32 TYR 0.025 0.002 TYR D 114 PHE 0.028 0.002 PHE D 270 TRP 0.021 0.002 TRP I 369 HIS 0.021 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00289 (24443) covalent geometry : angle 0.69635 (33270) hydrogen bonds : bond 0.03808 ( 1001) hydrogen bonds : angle 5.98173 ( 2841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.1974 (tmm) cc_final: 0.1251 (tmm) REVERT: B 68 TYR cc_start: 0.5672 (OUTLIER) cc_final: 0.4398 (m-80) REVERT: B 157 MET cc_start: 0.2025 (mtp) cc_final: 0.1812 (mtp) REVERT: C 7 ARG cc_start: 0.6550 (ttp-170) cc_final: 0.5928 (ttp-170) REVERT: C 289 MET cc_start: 0.4083 (pmm) cc_final: 0.2937 (tmm) REVERT: D 41 LEU cc_start: 0.5597 (mt) cc_final: 0.5265 (mp) REVERT: D 67 ILE cc_start: 0.4618 (OUTLIER) cc_final: 0.4338 (tt) REVERT: D 156 ARG cc_start: 0.2184 (ttt180) cc_final: 0.1584 (tmt170) REVERT: D 229 MET cc_start: 0.6415 (ptt) cc_final: 0.5439 (ptt) REVERT: E 109 MET cc_start: -0.1290 (mmm) cc_final: -0.1526 (mtm) REVERT: E 177 ARG cc_start: 0.6831 (mtm180) cc_final: 0.6570 (mtm180) REVERT: E 242 ARG cc_start: 0.3193 (ptm160) cc_final: 0.2304 (ttt-90) REVERT: F 175 MET cc_start: 0.3932 (tmm) cc_final: 0.3226 (ttm) REVERT: F 229 MET cc_start: 0.2118 (ttp) cc_final: 0.1881 (ttm) REVERT: F 289 MET cc_start: -0.2642 (OUTLIER) cc_final: -0.3061 (pmm) REVERT: G 123 MET cc_start: 0.0450 (OUTLIER) cc_final: 0.0009 (ptm) REVERT: G 138 MET cc_start: 0.0513 (mpp) cc_final: -0.1692 (ptm) REVERT: G 229 MET cc_start: 0.2476 (ptp) cc_final: 0.0020 (ptm) REVERT: H 54 HIS cc_start: 0.4027 (t-90) cc_final: 0.3671 (t-90) REVERT: H 157 MET cc_start: 0.3331 (ttp) cc_final: 0.2232 (mmp) REVERT: H 205 GLU cc_start: 0.5422 (mp0) cc_final: 0.4732 (pt0) REVERT: I 286 MET cc_start: 0.1942 (OUTLIER) cc_final: 0.1446 (ptp) REVERT: I 326 MET cc_start: 0.2507 (tpt) cc_final: 0.0084 (ptp) REVERT: I 343 MET cc_start: -0.3288 (mtp) cc_final: -0.3994 (tpt) REVERT: I 346 MET cc_start: -0.1475 (OUTLIER) cc_final: -0.2176 (mmm) REVERT: I 542 MET cc_start: 0.2172 (ppp) cc_final: 0.1755 (ptp) REVERT: J 50 GLN cc_start: 0.4674 (OUTLIER) cc_final: 0.2286 (mp10) REVERT: K 5 PRO cc_start: 0.8493 (Cg_endo) cc_final: 0.8264 (Cg_exo) REVERT: K 54 MET cc_start: 0.3647 (mpp) cc_final: 0.3091 (ptp) REVERT: K 106 MET cc_start: 0.1615 (tmm) cc_final: 0.1231 (tpt) outliers start: 64 outliers final: 37 residues processed: 300 average time/residue: 0.1478 time to fit residues: 71.7395 Evaluate side-chains 264 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 575 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 109 TYR Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 107 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 215 optimal weight: 0.0010 chunk 38 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 8 optimal weight: 0.0370 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN ** I 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN K 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.297562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.282048 restraints weight = 42190.531| |-----------------------------------------------------------------------------| r_work (start): 0.5067 rms_B_bonded: 2.58 r_work: 0.4988 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3499 moved from start: 1.0236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24443 Z= 0.122 Angle : 0.648 14.455 33270 Z= 0.332 Chirality : 0.046 0.290 3694 Planarity : 0.005 0.054 4206 Dihedral : 14.185 179.115 3891 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 19.38 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 2862 helix: 0.77 (0.17), residues: 961 sheet: -0.23 (0.23), residues: 508 loop : -1.01 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.018 0.002 TYR J 110 PHE 0.021 0.002 PHE D 270 TRP 0.019 0.002 TRP C 211 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00257 (24443) covalent geometry : angle 0.64754 (33270) hydrogen bonds : bond 0.03476 ( 1001) hydrogen bonds : angle 5.56294 ( 2841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2196 (tmm) cc_final: 0.1241 (tmm) REVERT: B 68 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.4219 (m-80) REVERT: B 157 MET cc_start: 0.1986 (mtp) cc_final: 0.1746 (mtp) REVERT: C 7 ARG cc_start: 0.6345 (ttp-170) cc_final: 0.5706 (ttp-170) REVERT: C 289 MET cc_start: 0.3732 (pmm) cc_final: 0.2704 (tmm) REVERT: D 41 LEU cc_start: 0.5654 (mt) cc_final: 0.5388 (mp) REVERT: D 229 MET cc_start: 0.6330 (ptt) cc_final: 0.5342 (ptt) REVERT: E 109 MET cc_start: -0.1327 (mmm) cc_final: -0.2265 (mtt) REVERT: E 242 ARG cc_start: 0.3309 (ptm160) cc_final: 0.2256 (ttt-90) REVERT: F 1 MET cc_start: 0.1426 (pmm) cc_final: 0.0794 (ptm) REVERT: F 9 GLU cc_start: -0.0072 (OUTLIER) cc_final: -0.2375 (mt-10) REVERT: F 175 MET cc_start: 0.4000 (tmm) cc_final: 0.3242 (ttm) REVERT: F 191 PHE cc_start: 0.3338 (OUTLIER) cc_final: 0.2565 (m-80) REVERT: G 229 MET cc_start: 0.2477 (ptp) cc_final: -0.0066 (ptm) REVERT: H 54 HIS cc_start: 0.3970 (t-90) cc_final: 0.3739 (t-170) REVERT: H 157 MET cc_start: 0.3220 (ttp) cc_final: 0.2093 (mmp) REVERT: H 205 GLU cc_start: 0.5449 (mp0) cc_final: 0.4751 (pt0) REVERT: I 286 MET cc_start: 0.1714 (OUTLIER) cc_final: 0.1220 (ptp) REVERT: I 326 MET cc_start: 0.2209 (tpt) cc_final: 0.0149 (ptp) REVERT: I 343 MET cc_start: -0.3183 (mtp) cc_final: -0.3950 (tpt) REVERT: I 346 MET cc_start: -0.1451 (OUTLIER) cc_final: -0.2523 (tpt) REVERT: I 542 MET cc_start: 0.1867 (ppp) cc_final: 0.1646 (ptp) REVERT: I 570 MET cc_start: 0.2969 (mtt) cc_final: 0.1739 (ptt) REVERT: J 50 GLN cc_start: 0.4892 (OUTLIER) cc_final: 0.2422 (mp10) REVERT: J 83 MET cc_start: 0.1529 (tpt) cc_final: 0.1181 (mtt) REVERT: K 5 PRO cc_start: 0.8538 (Cg_endo) cc_final: 0.8325 (Cg_exo) REVERT: K 106 MET cc_start: 0.1821 (tmm) cc_final: 0.0505 (mmm) outliers start: 55 outliers final: 34 residues processed: 279 average time/residue: 0.1521 time to fit residues: 68.0414 Evaluate side-chains 261 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 575 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 233 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 262 optimal weight: 0.1980 chunk 68 optimal weight: 0.0070 chunk 216 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.295169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.277604 restraints weight = 41814.174| |-----------------------------------------------------------------------------| r_work (start): 0.5038 rms_B_bonded: 2.45 r_work: 0.4972 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3654 moved from start: 1.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24443 Z= 0.146 Angle : 0.689 14.808 33270 Z= 0.352 Chirality : 0.047 0.227 3694 Planarity : 0.005 0.062 4206 Dihedral : 14.164 178.555 3891 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 19.38 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 2862 helix: 0.70 (0.16), residues: 958 sheet: -0.26 (0.23), residues: 497 loop : -1.10 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 24 TYR 0.028 0.002 TYR E 183 PHE 0.021 0.002 PHE J 117 TRP 0.016 0.002 TRP M 40 HIS 0.010 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00313 (24443) covalent geometry : angle 0.68870 (33270) hydrogen bonds : bond 0.03883 ( 1001) hydrogen bonds : angle 5.71177 ( 2841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2185 (tmm) cc_final: 0.1240 (tmm) REVERT: B 68 TYR cc_start: 0.5653 (OUTLIER) cc_final: 0.4353 (m-80) REVERT: C 7 ARG cc_start: 0.6439 (ttp-170) cc_final: 0.5683 (ttp-170) REVERT: C 9 GLU cc_start: 0.5921 (pt0) cc_final: 0.5331 (pt0) REVERT: C 138 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.2884 (mtt) REVERT: C 289 MET cc_start: 0.3662 (pmm) cc_final: 0.2588 (tmm) REVERT: D 22 ASN cc_start: 0.2602 (OUTLIER) cc_final: 0.2388 (t0) REVERT: D 41 LEU cc_start: 0.5881 (mt) cc_final: 0.5612 (mp) REVERT: D 217 MET cc_start: 0.1372 (tpt) cc_final: 0.0873 (tpt) REVERT: D 229 MET cc_start: 0.6513 (ptt) cc_final: 0.5711 (ptt) REVERT: E 109 MET cc_start: -0.1665 (mmm) cc_final: -0.2662 (mtt) REVERT: E 242 ARG cc_start: 0.3428 (ptm160) cc_final: 0.3049 (ttt180) REVERT: F 1 MET cc_start: 0.1535 (pmm) cc_final: 0.1121 (ptm) REVERT: F 9 GLU cc_start: -0.0192 (OUTLIER) cc_final: -0.2359 (mt-10) REVERT: F 175 MET cc_start: 0.3906 (tmm) cc_final: 0.3026 (ttm) REVERT: F 191 PHE cc_start: 0.3543 (OUTLIER) cc_final: 0.2779 (m-80) REVERT: G 229 MET cc_start: 0.2435 (ptp) cc_final: -0.0077 (ptm) REVERT: H 44 ASP cc_start: 0.4730 (p0) cc_final: 0.4148 (t0) REVERT: H 70 GLN cc_start: 0.4677 (tm-30) cc_final: 0.4377 (tm-30) REVERT: H 157 MET cc_start: 0.3185 (ttp) cc_final: 0.2105 (mmp) REVERT: H 205 GLU cc_start: 0.5472 (mp0) cc_final: 0.4771 (pt0) REVERT: I 286 MET cc_start: 0.1958 (OUTLIER) cc_final: 0.1391 (ptp) REVERT: I 326 MET cc_start: 0.2381 (tpt) cc_final: 0.0149 (ptp) REVERT: I 343 MET cc_start: -0.3136 (mtp) cc_final: -0.3929 (tpt) REVERT: I 346 MET cc_start: -0.1597 (OUTLIER) cc_final: -0.2717 (tpt) REVERT: I 570 MET cc_start: 0.2998 (mtt) cc_final: 0.1752 (ptt) REVERT: I 575 ILE cc_start: 0.1921 (OUTLIER) cc_final: 0.1667 (mt) REVERT: J 50 GLN cc_start: 0.4462 (OUTLIER) cc_final: 0.3913 (mm-40) REVERT: J 83 MET cc_start: 0.1915 (tpt) cc_final: 0.0856 (mtt) REVERT: J 87 ILE cc_start: 0.1393 (tp) cc_final: 0.1099 (tp) REVERT: J 89 ASN cc_start: 0.6716 (p0) cc_final: 0.6412 (p0) REVERT: K 5 PRO cc_start: 0.8659 (Cg_endo) cc_final: 0.8444 (Cg_exo) REVERT: K 106 MET cc_start: 0.2189 (tmm) cc_final: 0.1731 (mmt) REVERT: M 51 GLU cc_start: 0.4760 (OUTLIER) cc_final: 0.4289 (mp0) outliers start: 60 outliers final: 41 residues processed: 294 average time/residue: 0.1522 time to fit residues: 72.1570 Evaluate side-chains 272 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 575 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 163 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 172 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN I 222 ASN I 535 ASN ** J 53 HIS ** 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 = 0.5158 r_free = 0.5158 target = 0.289259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.269580 restraints weight = 40865.384| |-----------------------------------------------------------------------------| r_work (start): 0.4991 rms_B_bonded: 2.40 r_work: 0.4925 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3991 moved from start: 1.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24443 Z= 0.203 Angle : 0.827 16.521 33270 Z= 0.429 Chirality : 0.051 0.212 3694 Planarity : 0.007 0.109 4206 Dihedral : 14.498 177.126 3891 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 2.91 % Allowed : 19.62 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 2862 helix: 0.14 (0.16), residues: 955 sheet: -0.65 (0.23), residues: 477 loop : -1.36 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 64 TYR 0.039 0.003 TYR K 79 PHE 0.042 0.003 PHE H 210 TRP 0.028 0.002 TRP M 40 HIS 0.012 0.002 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00439 (24443) covalent geometry : angle 0.82652 (33270) hydrogen bonds : bond 0.04957 ( 1001) hydrogen bonds : angle 6.50196 ( 2841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2381 (tmm) cc_final: 0.1443 (tmm) REVERT: B 67 ILE cc_start: 0.6596 (mt) cc_final: 0.6033 (mt) REVERT: B 68 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5025 (m-80) REVERT: B 109 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5797 (mpp) REVERT: C 7 ARG cc_start: 0.6330 (ttp-170) cc_final: 0.5796 (mtp180) REVERT: C 9 GLU cc_start: 0.6175 (pt0) cc_final: 0.5951 (mp0) REVERT: C 12 LEU cc_start: 0.3855 (OUTLIER) cc_final: 0.2879 (mp) REVERT: C 138 MET cc_start: 0.4241 (OUTLIER) cc_final: 0.3579 (mmm) REVERT: C 289 MET cc_start: 0.3065 (pmm) cc_final: 0.1919 (tmm) REVERT: D 41 LEU cc_start: 0.6184 (mt) cc_final: 0.5864 (mp) REVERT: D 217 MET cc_start: 0.0757 (tpt) cc_final: 0.0405 (tpt) REVERT: E 17 GLU cc_start: 0.5194 (tp30) cc_final: 0.3872 (mm-30) REVERT: E 109 MET cc_start: -0.1076 (mmm) cc_final: -0.2454 (mtt) REVERT: E 138 MET cc_start: 0.3355 (OUTLIER) cc_final: 0.2531 (ptp) REVERT: F 1 MET cc_start: 0.2146 (pmm) cc_final: 0.1462 (ptm) REVERT: F 9 GLU cc_start: 0.0096 (OUTLIER) cc_final: -0.1726 (mt-10) REVERT: F 175 MET cc_start: 0.3961 (tmm) cc_final: 0.3004 (ttm) REVERT: F 191 PHE cc_start: 0.3501 (OUTLIER) cc_final: 0.2756 (m-80) REVERT: F 241 ASN cc_start: 0.1783 (OUTLIER) cc_final: 0.1550 (m-40) REVERT: G 229 MET cc_start: 0.2582 (ptp) cc_final: 0.0041 (ptm) REVERT: H 30 MET cc_start: 0.4599 (tpp) cc_final: 0.4258 (tpt) REVERT: H 157 MET cc_start: 0.3072 (ttp) cc_final: 0.2105 (mmt) REVERT: H 205 GLU cc_start: 0.5669 (mp0) cc_final: 0.4949 (pt0) REVERT: I 286 MET cc_start: 0.2980 (OUTLIER) cc_final: 0.2224 (ptp) REVERT: I 343 MET cc_start: -0.2674 (mtp) cc_final: -0.3465 (tpt) REVERT: I 346 MET cc_start: -0.1757 (OUTLIER) cc_final: -0.2981 (tpt) REVERT: I 570 MET cc_start: 0.3056 (mtt) cc_final: 0.1771 (ptt) REVERT: I 571 MET cc_start: 0.2645 (tpp) cc_final: 0.1780 (tpp) REVERT: I 575 ILE cc_start: 0.2206 (OUTLIER) cc_final: 0.1909 (mt) REVERT: I 597 TYR cc_start: 0.2482 (OUTLIER) cc_final: 0.1352 (t80) REVERT: J 83 MET cc_start: 0.2031 (tpt) cc_final: 0.0955 (mtt) REVERT: J 86 ILE cc_start: 0.4413 (mt) cc_final: 0.4107 (mt) REVERT: K 5 PRO cc_start: 0.8834 (Cg_endo) cc_final: 0.8628 (Cg_exo) REVERT: M 36 MET cc_start: 0.0718 (mmm) cc_final: 0.0273 (mmm) REVERT: M 51 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5624 (mp0) outliers start: 71 outliers final: 38 residues processed: 305 average time/residue: 0.1468 time to fit residues: 73.0991 Evaluate side-chains 273 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 286 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 575 ILE Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 252 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 0.0060 chunk 201 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 54 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS J 89 ASN ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.293689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.275134 restraints weight = 41519.283| |-----------------------------------------------------------------------------| r_work (start): 0.5021 rms_B_bonded: 2.41 r_work: 0.4957 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3844 moved from start: 1.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24443 Z= 0.134 Angle : 0.689 15.327 33270 Z= 0.350 Chirality : 0.046 0.212 3694 Planarity : 0.005 0.054 4206 Dihedral : 14.240 179.347 3891 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 2.09 % Allowed : 20.93 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 2862 helix: 0.57 (0.17), residues: 955 sheet: -0.46 (0.23), residues: 511 loop : -1.26 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG I 450 TYR 0.022 0.002 TYR J 110 PHE 0.038 0.002 PHE H 210 TRP 0.018 0.002 TRP I 369 HIS 0.007 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00286 (24443) covalent geometry : angle 0.68948 (33270) hydrogen bonds : bond 0.03794 ( 1001) hydrogen bonds : angle 5.77511 ( 2841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.2485 (tmm) cc_final: 0.1450 (tmm) REVERT: B 68 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.4181 (m-80) REVERT: C 7 ARG cc_start: 0.5932 (ttp-170) cc_final: 0.5565 (ttp-170) REVERT: C 138 MET cc_start: 0.4013 (OUTLIER) cc_final: 0.3586 (mtt) REVERT: C 289 MET cc_start: 0.2502 (pmm) cc_final: 0.2053 (ttp) REVERT: D 41 LEU cc_start: 0.6128 (mt) cc_final: 0.5886 (mp) REVERT: E 109 MET cc_start: -0.1619 (mmm) cc_final: -0.2751 (mtt) REVERT: E 138 MET cc_start: 0.3099 (OUTLIER) cc_final: 0.1967 (ptp) REVERT: F 1 MET cc_start: 0.1732 (pmm) cc_final: 0.1095 (ptm) REVERT: F 9 GLU cc_start: -0.0441 (OUTLIER) cc_final: -0.2197 (mt-10) REVERT: F 175 MET cc_start: 0.3978 (tmm) cc_final: 0.3030 (ttm) REVERT: F 191 PHE cc_start: 0.3377 (OUTLIER) cc_final: 0.2554 (m-80) REVERT: F 229 MET cc_start: 0.0232 (ttm) cc_final: -0.0410 (ttm) REVERT: G 229 MET cc_start: 0.2181 (ptp) cc_final: 0.0852 (ptt) REVERT: H 157 MET cc_start: 0.2998 (ttp) cc_final: 0.2009 (mmp) REVERT: H 205 GLU cc_start: 0.5706 (mp0) cc_final: 0.5082 (pt0) REVERT: I 10 TYR cc_start: 0.1207 (t80) cc_final: 0.0697 (t80) REVERT: I 343 MET cc_start: -0.2650 (mtp) cc_final: -0.3432 (tpt) REVERT: I 346 MET cc_start: -0.1526 (OUTLIER) cc_final: -0.2900 (tpt) REVERT: I 378 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.2280 (tt) REVERT: I 571 MET cc_start: 0.2297 (tpp) cc_final: 0.1592 (tpp) REVERT: J 83 MET cc_start: 0.1749 (tpt) cc_final: 0.0966 (mtt) REVERT: J 86 ILE cc_start: 0.4396 (mt) cc_final: 0.4051 (mt) REVERT: M 36 MET cc_start: 0.1101 (mmm) cc_final: 0.0222 (mmm) REVERT: M 51 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5697 (mp0) outliers start: 51 outliers final: 30 residues processed: 279 average time/residue: 0.1482 time to fit residues: 68.3678 Evaluate side-chains 253 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 186 TYR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 1 VAL Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 266 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN H 179 HIS I 221 ASN I 232 GLN ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 HIS ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.283230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.262313 restraints weight = 40054.213| |-----------------------------------------------------------------------------| r_work (start): 0.4927 rms_B_bonded: 2.36 r_work: 0.4859 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 moved from start: 1.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 24443 Z= 0.270 Angle : 0.967 18.035 33270 Z= 0.502 Chirality : 0.057 0.300 3694 Planarity : 0.007 0.089 4206 Dihedral : 14.981 176.936 3891 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.07 % Favored : 91.86 % Rotamer: Outliers : 2.21 % Allowed : 20.20 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 2862 helix: -0.32 (0.16), residues: 923 sheet: -0.84 (0.24), residues: 468 loop : -1.71 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 450 TYR 0.054 0.003 TYR C 186 PHE 0.040 0.004 PHE H 210 TRP 0.035 0.003 TRP C 211 HIS 0.025 0.003 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00604 (24443) covalent geometry : angle 0.96738 (33270) hydrogen bonds : bond 0.06269 ( 1001) hydrogen bonds : angle 7.21691 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6287.55 seconds wall clock time: 108 minutes 14.06 seconds (6494.06 seconds total)