Starting phenix.real_space_refine on Sun Sep 13 14:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfo_27409/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfo_27409/09_2026/8dfo_27409.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 4.80, per 1000 atoms: 0.20 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: 1.42 Conformation dependent library (CDL) restraints added in 900.2 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: 2.96 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: 4.11 Time building geometry restraints manager: 2.06 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: 14324 35.53 - 71.07: 412 71.07 - 106.60: 33 106.60 - 142.14: 2 142.14 - 177.67: 13 Dihedral angle restraints: 14784 sinusoidal: 6355 harmonic: 8429 Sorted by residual: dihedral pdb=" C4' U L 6 " pdb=" C3' U L 6 " pdb=" C2' U L 6 " pdb=" C1' U L 6 " ideal model delta sinusoidal sigma weight residual 36.34 -42.30 78.64 1 3.10e+00 1.04e-01 8.02e+02 dihedral pdb=" C4' G L 27 " pdb=" C3' G L 27 " pdb=" C2' G L 27 " pdb=" C1' G L 27 " ideal model delta sinusoidal sigma weight residual 36.34 -37.61 73.95 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' A L 10 " pdb=" C3' A L 10 " pdb=" C2' A L 10 " pdb=" C1' A L 10 " ideal model delta sinusoidal sigma weight residual 36.34 -32.47 68.81 1 3.10e+00 1.04e-01 6.38e+02 ... (remaining 14781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3300 0.148 - 0.296: 51 0.296 - 0.444: 84 0.444 - 0.592: 190 0.592 - 0.740: 69 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: 6.810 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.570 Find NCS groups from input model: 0.390 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0679 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= 1.190 Angle : 1.635 106.046 33270 Z= 0.954 Chirality : 0.168 0.740 3694 Planarity : 0.006 0.100 4206 Dihedral : 16.819 177.673 9326 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/Z covalent geometry : bond 0.02152 / 1.19 (24443) covalent geometry : angle 1.63519 / 0.95 (33270) hydrogen bonds : bond 0.18960 / 12.41 ( 1001) hydrogen bonds : angle 8.21135 / 5.72 ( 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 : 0.882 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: 0.1754 time to fit residues: 92.0978 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 : 0.629 ------------------------------------------------------------------------------- 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... 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 ** K 53 HIS ** 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 = 0.5262 r_free = 0.5262 target = 0.304227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.287915 restraints weight = 44157.750| |-----------------------------------------------------------------------------| r_work (start): 0.5127 rms_B_bonded: 2.78 r_work: 0.5056 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.5056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1006 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24443 Z= 0.153 Angle : 0.769 11.649 33270 Z= 0.372 Chirality : 0.059 0.735 3694 Planarity : 0.005 0.066 4206 Dihedral : 12.667 179.199 3722 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.17 % Allowed : 12.29 % Favored : 85.54 % 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: 0.31 (0.16), residues: 2862 helix: 1.43 (0.17), residues: 952 sheet: 0.39 (0.23), residues: 532 loop : -0.72 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.026 0.002 TYR I 10 PHE 0.031 0.002 PHE K 18 TRP 0.017 0.002 TRP M 31 HIS 0.008 0.001 HIS K 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (24443) covalent geometry : angle 0.76873 / 0.37 (33270) hydrogen bonds : bond 0.03742 / 2.57 ( 1001) hydrogen bonds : angle 5.60247 / 3.96 ( 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 301 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 0.826 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 14 ARG cc_start: 0.5782 (ttt180) cc_final: 0.5549 (tpt-90) REVERT: B 175 MET cc_start: 0.3673 (pmm) cc_final: 0.2108 (ptp) REVERT: C 30 MET cc_start: 0.0292 (mtp) cc_final: -0.0915 (mmm) REVERT: C 109 MET cc_start: 0.2195 (ppp) cc_final: -0.0447 (mtt) REVERT: C 123 MET cc_start: -0.2160 (ptp) cc_final: -0.3364 (ptp) REVERT: C 138 MET cc_start: 0.3840 (ppp) cc_final: -0.0042 (mtm) REVERT: C 175 MET cc_start: 0.2615 (tpp) cc_final: 0.2044 (mtm) REVERT: D 183 TYR cc_start: 0.2530 (t80) cc_final: 0.1452 (t80) REVERT: E 114 TYR cc_start: 0.4530 (t80) cc_final: 0.4062 (t80) REVERT: E 138 MET cc_start: 0.2869 (mtt) cc_final: 0.1052 (mpp) REVERT: F 1 MET cc_start: -0.0252 (ptm) cc_final: -0.2411 (mtp) REVERT: G 138 MET cc_start: -0.1721 (ptp) cc_final: -0.2835 (mtm) REVERT: H 41 LEU cc_start: 0.6282 (pp) cc_final: 0.5947 (pp) REVERT: I 343 MET cc_start: -0.2799 (mtp) cc_final: -0.4400 (tpt) REVERT: I 346 MET cc_start: -0.1003 (OUTLIER) cc_final: -0.1877 (mmm) REVERT: K 97 MET cc_start: -0.0679 (mmp) cc_final: -0.3493 (mmt) REVERT: M 1 MET cc_start: 0.3334 (mtt) cc_final: 0.2733 (ttp) outliers start: 53 outliers final: 21 residues processed: 282 average time/residue: 0.1643 time to fit residues: 72.6953 Evaluate side-chains 237 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 109 MET 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 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 255 VAL Chi-restraints excluded: chain F residue 45 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: 8.9990 chunk 229 optimal weight: 2.9990 chunk 275 optimal weight: 0.0980 chunk 114 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 210 optimal weight: 0.0570 chunk 175 optimal weight: 0.0070 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN C 70 GLN C 76 ASN C 220 HIS D 70 GLN E 216 ASN E 220 HIS ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 79 HIS I 183 GLN I 222 ASN I 327 HIS I 535 ASN I 538 GLN J 33 ASN J 84 GLN K 47 ASN ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.303953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5147 r_free = 0.5147 target = 0.289332 restraints weight = 43921.917| |-----------------------------------------------------------------------------| r_work (start): 0.5145 rms_B_bonded: 2.65 r_work: 0.5079 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1671 moved from start: 0.4370 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= 0.161 Angle : 0.762 12.054 33270 Z= 0.366 Chirality : 0.057 0.643 3694 Planarity : 0.005 0.086 4206 Dihedral : 12.675 178.497 3719 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.50 % Allowed : 12.95 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2862 helix: 1.41 (0.16), residues: 955 sheet: 0.40 (0.21), residues: 571 loop : -0.63 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 232 TYR 0.015 0.002 TYR B 273 PHE 0.026 0.002 PHE J 18 TRP 0.017 0.002 TRP M 40 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (24443) covalent geometry : angle 0.76215 / 0.37 (33270) hydrogen bonds : bond 0.03572 / 2.45 ( 1001) hydrogen bonds : angle 5.29538 / 3.76 ( 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 306 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.793 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: 0.3993 (mmm) cc_final: 0.3624 (mmm) REVERT: B 109 MET cc_start: 0.3808 (tmm) cc_final: 0.3384 (mpp) REVERT: B 175 MET cc_start: 0.3658 (pmm) cc_final: 0.2298 (ptp) REVERT: C 30 MET cc_start: 0.1039 (mtp) cc_final: -0.1780 (mtm) REVERT: C 123 MET cc_start: -0.1880 (ptp) cc_final: -0.3638 (mtm) REVERT: C 138 MET cc_start: 0.4028 (ppp) cc_final: 0.1765 (ppp) REVERT: C 175 MET cc_start: 0.2851 (tpp) cc_final: 0.2426 (mtm) REVERT: E 114 TYR cc_start: 0.3863 (t80) cc_final: 0.3405 (t80) REVERT: E 138 MET cc_start: 0.3274 (mtt) cc_final: 0.1505 (mpp) REVERT: G 138 MET cc_start: -0.1470 (ptp) cc_final: -0.3020 (mtm) REVERT: H 41 LEU cc_start: 0.6661 (pp) cc_final: 0.6458 (pp) REVERT: H 217 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5662 (ptt) REVERT: I 343 MET cc_start: -0.2910 (mtp) cc_final: -0.4238 (tpt) REVERT: I 346 MET cc_start: -0.1025 (OUTLIER) cc_final: -0.2340 (tpt) REVERT: I 363 ARG cc_start: 0.2852 (mtt-85) cc_final: 0.2164 (mtt180) REVERT: I 448 ARG cc_start: 0.2520 (OUTLIER) cc_final: 0.1218 (tpp-160) REVERT: I 514 GLU cc_start: 0.1163 (pt0) cc_final: 0.0574 (tt0) REVERT: K 14 LEU cc_start: 0.4232 (mt) cc_final: 0.3276 (mp) REVERT: K 97 MET cc_start: -0.0446 (mmp) cc_final: -0.1785 (mpp) outliers start: 61 outliers final: 31 residues processed: 289 average time/residue: 0.1608 time to fit residues: 73.6225 Evaluate side-chains 244 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B 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 138 MET Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain H residue 9 GLU 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 598 TYR Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL 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: 0.8980 chunk 288 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 GLN C 76 ASN C 241 ASN D 189 HIS E 245 ASN G 54 HIS I 221 ASN I 327 HIS J 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.303535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.290189 restraints weight = 43523.402| |-----------------------------------------------------------------------------| r_work (start): 0.5158 rms_B_bonded: 2.51 r_work: 0.5093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.5093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2266 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24443 Z= 0.174 Angle : 0.754 12.303 33270 Z= 0.368 Chirality : 0.056 0.604 3694 Planarity : 0.005 0.056 4206 Dihedral : 12.732 172.511 3719 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 2.54 % Allowed : 14.58 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2862 helix: 1.35 (0.16), residues: 965 sheet: 0.20 (0.22), residues: 533 loop : -0.60 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 156 TYR 0.015 0.002 TYR E 68 PHE 0.020 0.002 PHE F 113 TRP 0.019 0.002 TRP M 40 HIS 0.011 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (24443) covalent geometry : angle 0.75442 / 0.37 (33270) hydrogen bonds : bond 0.03568 / 2.45 ( 1001) hydrogen bonds : angle 5.25850 / 3.75 ( 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 315 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.5832 (mmm) cc_final: 0.5353 (tpp) REVERT: A 129 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6830 (t) REVERT: B 1 MET cc_start: 0.2202 (tmm) cc_final: 0.0277 (ppp) REVERT: C 30 MET cc_start: 0.2080 (mtp) cc_final: -0.1173 (mtm) REVERT: C 123 MET cc_start: -0.2103 (ptp) cc_final: -0.2634 (mtm) REVERT: C 138 MET cc_start: 0.4616 (OUTLIER) cc_final: 0.1450 (ptt) REVERT: C 175 MET cc_start: 0.2505 (tpp) cc_final: 0.2243 (mtt) REVERT: E 114 TYR cc_start: 0.3626 (t80) cc_final: 0.3301 (t80) REVERT: E 138 MET cc_start: 0.3682 (mtt) cc_final: 0.1881 (mpp) REVERT: F 179 HIS cc_start: 0.4527 (m-70) cc_final: 0.3784 (m170) REVERT: F 229 MET cc_start: 0.2036 (mtp) cc_final: -0.1908 (ptp) REVERT: G 138 MET cc_start: -0.1609 (ptp) cc_final: -0.3545 (mtm) REVERT: H 157 MET cc_start: 0.3352 (OUTLIER) cc_final: 0.2434 (mmt) REVERT: I 326 MET cc_start: 0.2088 (tpt) cc_final: -0.0282 (ptp) REVERT: I 334 ARG cc_start: 0.3011 (mtt180) cc_final: 0.2514 (tmm160) REVERT: I 343 MET cc_start: -0.2548 (mtp) cc_final: -0.4018 (tpt) REVERT: I 346 MET cc_start: -0.1159 (OUTLIER) cc_final: -0.2386 (tpt) REVERT: I 514 GLU cc_start: 0.1168 (pt0) cc_final: 0.0635 (tt0) REVERT: I 570 MET cc_start: 0.3355 (mtt) cc_final: 0.3111 (mtt) REVERT: I 594 MET cc_start: 0.0192 (mmp) cc_final: -0.0094 (tpp) REVERT: K 14 LEU cc_start: 0.4947 (mt) cc_final: 0.4093 (mp) REVERT: M 51 GLU cc_start: 0.3713 (OUTLIER) cc_final: 0.2877 (mp0) outliers start: 62 outliers final: 32 residues processed: 295 average time/residue: 0.1585 time to fit residues: 74.1776 Evaluate side-chains 253 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE 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 138 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 277 VAL 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 204 ASP Chi-restraints excluded: chain E residue 45 VAL 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 191 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 156 ARG Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 191 PHE 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 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 54 MET 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: 8.9990 chunk 141 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 195 optimal weight: 0.0040 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 241 ASN C 245 ASN 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN I 327 HIS I 360 ASN I 535 ASN I 538 GLN I 546 ASN I 572 GLN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.294690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.277895 restraints weight = 42147.425| |-----------------------------------------------------------------------------| r_work (start): 0.5046 rms_B_bonded: 2.44 r_work: 0.4979 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3599 moved from start: 0.9562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 24443 Z= 0.305 Angle : 1.118 17.211 33270 Z= 0.557 Chirality : 0.069 0.594 3694 Planarity : 0.008 0.097 4206 Dihedral : 13.822 179.459 3719 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 4.01 % Allowed : 16.47 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.31 (0.15), residues: 2862 helix: -0.21 (0.16), residues: 945 sheet: -0.46 (0.24), residues: 478 loop : -1.43 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 107 TYR 0.037 0.004 TYR B 183 PHE 0.035 0.004 PHE J 105 TRP 0.036 0.004 TRP M 40 HIS 0.013 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.30 (24443) covalent geometry : angle 1.11796 / 0.56 (33270) hydrogen bonds : bond 0.06251 / 4.26 ( 1001) hydrogen bonds : angle 7.15151 / 5.11 ( 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 345 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 247 time to evaluate : 0.778 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 181 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: B 1 MET cc_start: 0.2632 (tmm) cc_final: 0.1815 (ttp) REVERT: B 9 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: B 68 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.4859 (m-80) REVERT: C 7 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6055 (ttp-170) REVERT: C 123 MET cc_start: -0.0190 (ptp) cc_final: -0.2312 (mmm) REVERT: C 138 MET cc_start: 0.4740 (OUTLIER) cc_final: 0.2816 (mmm) REVERT: C 175 MET cc_start: 0.3043 (tpp) cc_final: 0.1895 (mtp) REVERT: C 229 MET cc_start: 0.1174 (mmt) cc_final: 0.0884 (mmt) REVERT: C 289 MET cc_start: 0.4532 (pmm) cc_final: 0.3119 (tmm) REVERT: D 145 GLU cc_start: 0.3995 (OUTLIER) cc_final: 0.3629 (tt0) REVERT: D 235 ILE cc_start: -0.2392 (OUTLIER) cc_final: -0.2919 (mp) REVERT: D 240 GLN cc_start: -0.0775 (OUTLIER) cc_final: -0.1104 (mm-40) REVERT: E 109 MET cc_start: -0.1384 (mmm) cc_final: -0.1874 (mtm) REVERT: E 242 ARG cc_start: 0.4141 (ptm160) cc_final: 0.3455 (ttt180) REVERT: F 9 GLU cc_start: 0.0751 (OUTLIER) cc_final: -0.1506 (mm-30) REVERT: F 175 MET cc_start: 0.3786 (tmm) cc_final: 0.3085 (ttp) REVERT: F 191 PHE cc_start: 0.3780 (OUTLIER) cc_final: 0.3169 (m-80) REVERT: G 119 PHE cc_start: 0.6268 (m-80) cc_final: 0.5721 (m-80) REVERT: H 157 MET cc_start: 0.3621 (ttp) cc_final: 0.2488 (mmp) REVERT: H 205 GLU cc_start: 0.5558 (mp0) cc_final: 0.4808 (pt0) REVERT: I 192 LYS cc_start: 0.6306 (mttt) cc_final: 0.6000 (mmtm) REVERT: I 228 TYR cc_start: 0.7698 (m-80) cc_final: 0.7336 (m-80) REVERT: I 343 MET cc_start: -0.2887 (mtp) cc_final: -0.4038 (tpt) REVERT: I 346 MET cc_start: -0.1632 (mmt) cc_final: -0.2332 (mmm) REVERT: I 408 ARG cc_start: 0.4280 (OUTLIER) cc_final: 0.2621 (ttm-80) REVERT: J 52 PHE cc_start: -0.0610 (OUTLIER) cc_final: -0.1140 (m-80) REVERT: J 106 MET cc_start: 0.4823 (mpp) cc_final: 0.4484 (mmt) REVERT: K 5 PRO cc_start: 0.8168 (Cg_endo) cc_final: 0.7831 (Cg_exo) REVERT: M 51 GLU cc_start: 0.4782 (OUTLIER) cc_final: 0.4308 (mp0) outliers start: 98 outliers final: 50 residues processed: 327 average time/residue: 0.1488 time to fit residues: 78.1717 Evaluate side-chains 275 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 196 LEU 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 123 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 240 GLN 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 37 THR Chi-restraints excluded: chain F residue 115 ASP 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 202 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 289 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 281 ASP Chi-restraints excluded: chain I residue 408 ARG Chi-restraints excluded: chain I residue 597 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 52 PHE Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 53 HIS 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: 2.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 277 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 222 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN B 112 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 239 HIS F 39 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN H 70 GLN I 535 ASN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.298468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.282856 restraints weight = 42437.874| |-----------------------------------------------------------------------------| r_work (start): 0.5082 rms_B_bonded: 2.46 r_work: 0.5017 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.5017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3402 moved from start: 0.9529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24443 Z= 0.140 Angle : 0.771 15.691 33270 Z= 0.371 Chirality : 0.056 0.542 3694 Planarity : 0.005 0.055 4206 Dihedral : 13.041 179.506 3719 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 2.42 % Allowed : 18.76 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2862 helix: 0.56 (0.16), residues: 967 sheet: -0.46 (0.22), residues: 516 loop : -1.06 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.020 0.002 TYR K 79 PHE 0.027 0.002 PHE D 270 TRP 0.021 0.002 TRP B 108 HIS 0.007 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (24443) covalent geometry : angle 0.77058 / 0.37 (33270) hydrogen bonds : bond 0.03730 / 2.55 ( 1001) hydrogen bonds : angle 5.86213 / 4.19 ( 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 308 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.3764 (tp40) cc_final: 0.3214 (tp40) REVERT: B 1 MET cc_start: 0.2971 (tmm) cc_final: 0.2230 (ttp) REVERT: B 68 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.4570 (m-80) REVERT: B 157 MET cc_start: 0.2767 (mtp) cc_final: 0.2395 (mtp) REVERT: C 7 ARG cc_start: 0.6523 (ttp-170) cc_final: 0.5710 (ttp-170) REVERT: C 138 MET cc_start: 0.4015 (OUTLIER) cc_final: 0.3675 (ppp) REVERT: C 175 MET cc_start: 0.2797 (tpp) cc_final: 0.1826 (mtp) REVERT: C 289 MET cc_start: 0.3962 (pmm) cc_final: 0.2716 (tmm) REVERT: D 41 LEU cc_start: 0.5516 (mt) cc_final: 0.5210 (mp) REVERT: D 67 ILE cc_start: 0.4708 (OUTLIER) cc_final: 0.4400 (tt) REVERT: E 242 ARG cc_start: 0.3162 (ptm160) cc_final: 0.2362 (ttm-80) REVERT: F 175 MET cc_start: 0.3723 (tmm) cc_final: 0.3439 (tpp) REVERT: F 191 PHE cc_start: 0.3282 (OUTLIER) cc_final: 0.3081 (m-80) REVERT: F 289 MET cc_start: -0.2833 (OUTLIER) cc_final: -0.3136 (pmm) REVERT: G 119 PHE cc_start: 0.6082 (m-80) cc_final: 0.5525 (m-80) REVERT: H 44 ASP cc_start: 0.5118 (p0) cc_final: 0.3586 (t0) REVERT: H 54 HIS cc_start: 0.3967 (t-90) cc_final: 0.3638 (t-90) REVERT: H 138 MET cc_start: 0.3947 (tmm) cc_final: 0.3388 (tmm) REVERT: H 157 MET cc_start: 0.3460 (ttp) cc_final: 0.2272 (mmp) REVERT: H 205 GLU cc_start: 0.5559 (mp0) cc_final: 0.4910 (pt0) REVERT: H 210 PHE cc_start: 0.3931 (t80) cc_final: 0.3497 (t80) REVERT: I 343 MET cc_start: -0.3173 (mtp) cc_final: -0.3955 (tpt) REVERT: I 346 MET cc_start: -0.1679 (OUTLIER) cc_final: -0.2286 (mmm) REVERT: I 571 MET cc_start: 0.0441 (mmp) cc_final: -0.0014 (tpp) REVERT: J 50 GLN cc_start: 0.4365 (OUTLIER) cc_final: 0.2017 (mp10) REVERT: J 111 HIS cc_start: 0.1689 (OUTLIER) cc_final: -0.0678 (p90) REVERT: K 106 MET cc_start: 0.1135 (tpt) cc_final: -0.0424 (mpp) REVERT: M 51 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.4355 (mp0) outliers start: 59 outliers final: 30 residues processed: 293 average time/residue: 0.1401 time to fit residues: 66.6119 Evaluate side-chains 258 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 30 MET 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 C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE 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 191 PHE Chi-restraints excluded: chain E residue 45 VAL 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 191 PHE Chi-restraints excluded: chain F residue 289 MET Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 575 ILE 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 54 MET 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 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 107 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** D 239 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** G 239 HIS ** H 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.285840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.266031 restraints weight = 40453.466| |-----------------------------------------------------------------------------| r_work (start): 0.4961 rms_B_bonded: 2.40 r_work: 0.4893 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4144 moved from start: 1.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.153 24443 Z= 0.303 Angle : 1.144 19.954 33270 Z= 0.570 Chirality : 0.072 0.680 3694 Planarity : 0.008 0.068 4206 Dihedral : 13.943 173.789 3719 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.34 % Favored : 92.56 % Rotamer: Outliers : 3.81 % Allowed : 18.93 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 2862 helix: -0.61 (0.16), residues: 931 sheet: -0.92 (0.23), residues: 504 loop : -1.76 (0.15), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 226 TYR 0.039 0.004 TYR A 34 PHE 0.044 0.004 PHE E 14 TRP 0.042 0.003 TRP M 40 HIS 0.029 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (24443) covalent geometry : angle 1.14368 / 0.57 (33270) hydrogen bonds : bond 0.06984 / 4.78 ( 1001) hydrogen bonds : angle 7.60462 / 5.39 ( 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 340 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 247 time to evaluate : 0.623 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 57 LEU cc_start: 0.7432 (mp) cc_final: 0.7216 (mt) REVERT: B 68 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: B 157 MET cc_start: 0.2610 (mtp) cc_final: 0.1580 (mpp) REVERT: C 7 ARG cc_start: 0.6675 (ttp-170) cc_final: 0.5497 (ttp-170) REVERT: C 138 MET cc_start: 0.4809 (OUTLIER) cc_final: 0.3843 (mmt) REVERT: C 175 MET cc_start: 0.3217 (tpp) cc_final: 0.2448 (mtp) REVERT: C 289 MET cc_start: 0.3808 (pmm) cc_final: 0.2600 (tmm) REVERT: D 41 LEU cc_start: 0.6153 (mt) cc_final: 0.5825 (mp) REVERT: D 211 TRP cc_start: 0.0364 (OUTLIER) cc_final: -0.1131 (m100) REVERT: D 229 MET cc_start: 0.6990 (ptt) cc_final: 0.6666 (ptt) REVERT: D 282 GLU cc_start: 0.4154 (OUTLIER) cc_final: 0.3678 (pm20) REVERT: F 9 GLU cc_start: 0.0891 (OUTLIER) cc_final: -0.1308 (mm-30) REVERT: F 157 MET cc_start: 0.0490 (ptt) cc_final: -0.0450 (ptt) REVERT: F 175 MET cc_start: 0.3488 (tmm) cc_final: 0.2757 (ttm) REVERT: F 191 PHE cc_start: 0.3660 (OUTLIER) cc_final: 0.2900 (m-80) REVERT: F 217 MET cc_start: 0.2272 (mtt) cc_final: 0.0816 (mtm) REVERT: F 229 MET cc_start: 0.0762 (ttm) cc_final: 0.0449 (ttm) REVERT: G 136 VAL cc_start: 0.6441 (OUTLIER) cc_final: 0.6202 (p) REVERT: G 235 ILE cc_start: -0.0381 (OUTLIER) cc_final: -0.0823 (mm) REVERT: H 76 ASN cc_start: 0.3107 (m-40) cc_final: 0.1661 (p0) REVERT: H 119 PHE cc_start: 0.3154 (p90) cc_final: 0.2929 (t80) REVERT: H 157 MET cc_start: 0.3258 (ttp) cc_final: 0.2075 (mmp) REVERT: H 205 GLU cc_start: 0.5782 (mp0) cc_final: 0.5313 (pt0) REVERT: I 201 ILE cc_start: 0.0845 (OUTLIER) cc_final: 0.0198 (mt) REVERT: I 343 MET cc_start: -0.3106 (mtp) cc_final: -0.3813 (tpt) REVERT: I 571 MET cc_start: 0.0914 (mmp) cc_final: 0.0418 (tpp) REVERT: I 597 TYR cc_start: 0.2296 (OUTLIER) cc_final: 0.1238 (t80) REVERT: I 598 TYR cc_start: 0.2586 (OUTLIER) cc_final: 0.1099 (p90) REVERT: J 106 MET cc_start: 0.5267 (mpp) cc_final: 0.4755 (mpp) REVERT: K 106 MET cc_start: 0.1893 (tpt) cc_final: 0.1618 (mmt) REVERT: M 31 TRP cc_start: 0.0776 (OUTLIER) cc_final: 0.0084 (t60) REVERT: M 51 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.4858 (mp0) outliers start: 93 outliers final: 49 residues processed: 326 average time/residue: 0.1493 time to fit residues: 77.6862 Evaluate side-chains 268 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 200 ASP 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 263 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 191 PHE Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 ILE 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 202 PHE Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 524 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 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 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 53 HIS Chi-restraints excluded: chain K residue 95 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 233 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 22 ASN C 54 HIS D 220 HIS D 239 HIS E 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 HIS H 22 ASN ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN I 393 GLN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.290800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.272191 restraints weight = 41125.844| |-----------------------------------------------------------------------------| r_work (start): 0.5006 rms_B_bonded: 2.39 r_work: 0.4941 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3993 moved from start: 1.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24443 Z= 0.164 Angle : 0.827 17.620 33270 Z= 0.403 Chirality : 0.058 0.545 3694 Planarity : 0.006 0.077 4206 Dihedral : 13.208 173.134 3719 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 2.58 % Allowed : 20.52 % Favored : 76.89 % 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: -1.37 (0.15), residues: 2862 helix: 0.04 (0.16), residues: 943 sheet: -0.99 (0.22), residues: 519 loop : -1.51 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 142 TYR 0.024 0.002 TYR D 114 PHE 0.022 0.002 PHE E 14 TRP 0.017 0.002 TRP I 369 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (24443) covalent geometry : angle 0.82654 / 0.40 (33270) hydrogen bonds : bond 0.04456 / 3.07 ( 1001) hydrogen bonds : angle 6.45739 / 4.57 ( 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 289 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 226 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.5203 (m-80) REVERT: C 7 ARG cc_start: 0.6302 (ttp-170) cc_final: 0.5601 (ttp-170) REVERT: C 17 GLU cc_start: 0.2590 (tm-30) cc_final: 0.2136 (mp0) REVERT: C 138 MET cc_start: 0.4103 (OUTLIER) cc_final: 0.3739 (mmm) REVERT: C 175 MET cc_start: 0.3454 (tpp) cc_final: 0.2617 (mtp) REVERT: C 289 MET cc_start: 0.3348 (pmm) cc_final: 0.2146 (tmm) REVERT: D 41 LEU cc_start: 0.6050 (mt) cc_final: 0.5724 (mp) REVERT: D 229 MET cc_start: 0.6497 (ptt) cc_final: 0.5812 (ptt) REVERT: E 229 MET cc_start: 0.5709 (mmm) cc_final: 0.5285 (mmt) REVERT: F 9 GLU cc_start: 0.0067 (OUTLIER) cc_final: -0.1696 (mm-30) REVERT: F 107 ASP cc_start: 0.2784 (m-30) cc_final: 0.2367 (m-30) REVERT: F 191 PHE cc_start: 0.3214 (OUTLIER) cc_final: 0.2522 (m-80) REVERT: F 229 MET cc_start: 0.0582 (ttm) cc_final: 0.0253 (ttm) REVERT: G 136 VAL cc_start: 0.6124 (OUTLIER) cc_final: 0.5845 (p) REVERT: G 138 MET cc_start: -0.2665 (ptt) cc_final: -0.3249 (mpp) REVERT: H 119 PHE cc_start: 0.3342 (p90) cc_final: 0.3113 (t80) REVERT: H 157 MET cc_start: 0.3140 (ttp) cc_final: 0.2140 (mmt) REVERT: H 205 GLU cc_start: 0.5574 (mp0) cc_final: 0.5148 (pt0) REVERT: H 210 PHE cc_start: 0.3777 (t80) cc_final: 0.3254 (t80) REVERT: I 201 ILE cc_start: 0.1215 (OUTLIER) cc_final: 0.0380 (mt) REVERT: I 343 MET cc_start: -0.3314 (mtp) cc_final: -0.4133 (tpt) REVERT: I 571 MET cc_start: 0.0249 (mmp) cc_final: 0.0031 (tpp) REVERT: I 592 LEU cc_start: 0.4405 (OUTLIER) cc_final: 0.4205 (mt) REVERT: I 598 TYR cc_start: 0.2740 (OUTLIER) cc_final: 0.1584 (p90) REVERT: J 111 HIS cc_start: 0.1462 (OUTLIER) cc_final: -0.0896 (p90) outliers start: 63 outliers final: 35 residues processed: 280 average time/residue: 0.1485 time to fit residues: 66.9042 Evaluate side-chains 251 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL 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 191 PHE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 GLU 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 202 PHE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 592 LEU Chi-restraints excluded: chain I residue 598 TYR 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 111 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 163 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.0070 chunk 69 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 572 GLN J 53 HIS J 89 ASN ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5170 r_free = 0.5170 target = 0.291039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.272343 restraints weight = 41149.961| |-----------------------------------------------------------------------------| r_work (start): 0.5010 rms_B_bonded: 2.42 r_work: 0.4944 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4005 moved from start: 1.2255 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= 0.155 Angle : 0.797 16.636 33270 Z= 0.388 Chirality : 0.056 0.559 3694 Planarity : 0.006 0.069 4206 Dihedral : 12.968 173.302 3719 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.55 % Rotamer: Outliers : 2.09 % Allowed : 20.48 % Favored : 77.43 % 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: 0.32 (0.16), residues: 948 sheet: -0.86 (0.22), residues: 532 loop : -1.42 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 7 TYR 0.024 0.002 TYR D 114 PHE 0.027 0.002 PHE A 145 TRP 0.026 0.002 TRP C 211 HIS 0.010 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (24443) covalent geometry : angle 0.79719 / 0.39 (33270) hydrogen bonds : bond 0.04214 / 2.90 ( 1001) hydrogen bonds : angle 6.13763 / 4.35 ( 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 278 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 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: A 98 TYR cc_start: 0.5007 (OUTLIER) cc_final: 0.3923 (p90) REVERT: A 185 LYS cc_start: 0.7503 (tppp) cc_final: 0.7239 (tmtt) REVERT: B 68 TYR cc_start: 0.5244 (OUTLIER) cc_final: 0.4954 (m-80) REVERT: C 138 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3648 (mtt) REVERT: C 175 MET cc_start: 0.3162 (tpp) cc_final: 0.2666 (mtp) REVERT: C 289 MET cc_start: 0.2224 (pmm) cc_final: 0.1862 (tmm) REVERT: D 41 LEU cc_start: 0.6094 (mt) cc_final: 0.5788 (mp) REVERT: D 229 MET cc_start: 0.6481 (ptt) cc_final: 0.5760 (ptt) REVERT: E 229 MET cc_start: 0.5576 (mmm) cc_final: 0.5242 (mmt) REVERT: F 107 ASP cc_start: 0.2702 (m-30) cc_final: 0.2232 (m-30) REVERT: F 229 MET cc_start: 0.0533 (ttm) cc_final: 0.0312 (ttm) REVERT: G 136 VAL cc_start: 0.5757 (OUTLIER) cc_final: 0.5477 (p) REVERT: G 138 MET cc_start: -0.2897 (ptt) cc_final: -0.3164 (mpp) REVERT: G 157 MET cc_start: 0.4646 (tmm) cc_final: 0.4020 (ptp) REVERT: H 119 PHE cc_start: 0.3395 (p90) cc_final: 0.2992 (t80) REVERT: H 157 MET cc_start: 0.3054 (ttp) cc_final: 0.2117 (mmt) REVERT: H 205 GLU cc_start: 0.5567 (mp0) cc_final: 0.5179 (pt0) REVERT: H 210 PHE cc_start: 0.3860 (t80) cc_final: 0.3330 (t80) REVERT: I 201 ILE cc_start: 0.1891 (OUTLIER) cc_final: 0.1302 (mp) REVERT: I 343 MET cc_start: -0.3377 (mtp) cc_final: -0.3845 (tpt) REVERT: I 346 MET cc_start: -0.2283 (mmp) cc_final: -0.2987 (tpt) REVERT: I 571 MET cc_start: 0.0526 (mmp) cc_final: 0.0296 (tpp) REVERT: I 598 TYR cc_start: 0.2806 (OUTLIER) cc_final: 0.1782 (p90) REVERT: J 83 MET cc_start: 0.1497 (tpt) cc_final: 0.0857 (mtt) REVERT: J 87 ILE cc_start: 0.1602 (tp) cc_final: 0.1398 (tp) REVERT: J 111 HIS cc_start: 0.1465 (OUTLIER) cc_final: -0.0963 (p90) outliers start: 51 outliers final: 33 residues processed: 269 average time/residue: 0.1421 time to fit residues: 62.8940 Evaluate side-chains 256 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 17 GLU 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 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 191 PHE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 1 MET 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 202 PHE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 TYR 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 J residue 98 SER Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 69 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 80 optimal weight: 0.0170 chunk 184 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 201 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 HIS ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.293731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.275719 restraints weight = 41700.312| |-----------------------------------------------------------------------------| r_work (start): 0.5028 rms_B_bonded: 2.45 r_work: 0.4963 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3917 moved from start: 1.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24443 Z= 0.134 Angle : 0.747 15.480 33270 Z= 0.364 Chirality : 0.054 0.523 3694 Planarity : 0.006 0.067 4206 Dihedral : 12.781 175.578 3719 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 1.88 % Allowed : 20.93 % Favored : 77.18 % 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: -0.85 (0.15), residues: 2862 helix: 0.56 (0.16), residues: 958 sheet: -0.60 (0.22), residues: 545 loop : -1.34 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 450 TYR 0.018 0.001 TYR I 246 PHE 0.022 0.002 PHE A 145 TRP 0.024 0.002 TRP I 369 HIS 0.012 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24443) covalent geometry : angle 0.74690 / 0.36 (33270) hydrogen bonds : bond 0.03748 / 2.56 ( 1001) hydrogen bonds : angle 5.78518 / 4.11 ( 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 272 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.7541 (tppp) cc_final: 0.7279 (tmtt) REVERT: B 1 MET cc_start: 0.2459 (ttp) cc_final: 0.2067 (ttp) REVERT: B 68 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: C 17 GLU cc_start: 0.3322 (tm-30) cc_final: 0.2640 (mp0) REVERT: C 138 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.3613 (mtt) REVERT: C 175 MET cc_start: 0.3131 (tpp) cc_final: 0.2866 (mtp) REVERT: D 41 LEU cc_start: 0.6159 (mt) cc_final: 0.5823 (mp) REVERT: D 229 MET cc_start: 0.6378 (ptt) cc_final: 0.5711 (ptt) REVERT: E 181 VAL cc_start: 0.4021 (t) cc_final: 0.3342 (m) REVERT: F 107 ASP cc_start: 0.2331 (m-30) cc_final: 0.1840 (m-30) REVERT: G 136 VAL cc_start: 0.5717 (OUTLIER) cc_final: 0.5407 (p) REVERT: G 157 MET cc_start: 0.4789 (tmm) cc_final: 0.3723 (ptt) REVERT: H 119 PHE cc_start: 0.3430 (p90) cc_final: 0.3091 (t80) REVERT: H 157 MET cc_start: 0.3082 (ttp) cc_final: 0.2132 (mmp) REVERT: H 205 GLU cc_start: 0.5673 (mp0) cc_final: 0.5314 (pt0) REVERT: H 210 PHE cc_start: 0.3842 (t80) cc_final: 0.3343 (t80) REVERT: I 343 MET cc_start: -0.3149 (mtp) cc_final: -0.3906 (tpt) REVERT: I 346 MET cc_start: -0.2308 (mmp) cc_final: -0.3019 (tpt) REVERT: I 598 TYR cc_start: 0.3209 (OUTLIER) cc_final: 0.2591 (p90) REVERT: J 50 GLN cc_start: 0.4472 (OUTLIER) cc_final: 0.3844 (mm-40) REVERT: J 83 MET cc_start: 0.1366 (tpt) cc_final: 0.0797 (mtt) REVERT: J 87 ILE cc_start: 0.1819 (tp) cc_final: 0.1618 (tp) REVERT: J 111 HIS cc_start: 0.1475 (OUTLIER) cc_final: -0.0828 (p90) outliers start: 46 outliers final: 34 residues processed: 261 average time/residue: 0.1544 time to fit residues: 66.1841 Evaluate side-chains 255 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 17 GLU 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 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 191 PHE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 GLU 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 G residue 33 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 470 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 266 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 HIS ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5174 r_free = 0.5174 target = 0.291542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.273408 restraints weight = 41220.321| |-----------------------------------------------------------------------------| r_work (start): 0.5019 rms_B_bonded: 2.61 r_work: 0.4935 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 moved from start: 1.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24443 Z= 0.150 Angle : 0.776 15.147 33270 Z= 0.380 Chirality : 0.055 0.523 3694 Planarity : 0.006 0.077 4206 Dihedral : 12.748 174.994 3719 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 1.84 % Allowed : 21.02 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2862 helix: 0.50 (0.16), residues: 965 sheet: -0.47 (0.22), residues: 529 loop : -1.33 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 107 TYR 0.024 0.002 TYR D 114 PHE 0.026 0.002 PHE A 145 TRP 0.023 0.002 TRP C 211 HIS 0.013 0.002 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (24443) covalent geometry : angle 0.77642 / 0.38 (33270) hydrogen bonds : bond 0.04033 / 2.75 ( 1001) hydrogen bonds : angle 5.83102 / 4.14 ( 2841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6202.01 seconds wall clock time: 107 minutes 0.11 seconds (6420.11 seconds total)