Starting phenix.real_space_refine on Wed May 21 15:20:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2y_38022/05_2025/8x2y_38022.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.020 sd= 0.471 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5443 atoms to isotropic. 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 290 5.49 5 S 22 5.16 5 C 10104 2.51 5 N 3123 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17396 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "K" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2357 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 465 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain breaks: 1 Chain: "M" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1831 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Time building chain proxies: 9.63, per 1000 atoms: 0.55 Number of scatterers: 17396 At special positions: 0 Unit cell: (152.88, 137.28, 133.12, 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 22 16.00 P 290 15.00 O 3857 8.00 N 3123 7.00 C 10104 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: 4.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2684 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 7 sheets defined 57.7% alpha, 2.5% beta 143 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 7.14 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.116A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.626A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.748A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.450A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP B 68 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.063A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.570A pdb=" N ILE C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 66 removed outlier: 3.988A pdb=" N LEU C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 63 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 80 through 86 Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.131A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 60 through 87 Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.872A pdb=" N LEU D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.696A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.654A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 5.239A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 33 through 41 removed outlier: 5.152A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 27 through 39 removed outlier: 3.882A pdb=" N ILE G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 62 removed outlier: 3.723A pdb=" N THR G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 68 through 74 removed outlier: 3.756A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS G 73 " --> pdb=" O GLY G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.524A pdb=" N LEU G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU G 87 " --> pdb=" O ARG G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 40 through 52 Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.823A pdb=" N LEU H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.739A pdb=" N SER H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 191 removed outlier: 4.125A pdb=" N THR K 190 " --> pdb=" O PRO K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 removed outlier: 3.657A pdb=" N ARG K 215 " --> pdb=" O TYR K 211 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS K 216 " --> pdb=" O GLU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 256 removed outlier: 3.964A pdb=" N CYS K 252 " --> pdb=" O CYS K 248 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU K 253 " --> pdb=" O ARG K 249 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 327 Processing helix chain 'K' and resid 327 through 332 removed outlier: 3.554A pdb=" N GLU K 331 " --> pdb=" O LEU K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 363 removed outlier: 3.651A pdb=" N TRP K 353 " --> pdb=" O TYR K 349 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 359 " --> pdb=" O ASP K 355 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 377 removed outlier: 3.636A pdb=" N SER K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 386 removed outlier: 3.610A pdb=" N ILE K 384 " --> pdb=" O THR K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 415 Processing helix chain 'L' and resid 6 through 31 removed outlier: 3.572A pdb=" N ALA L 13 " --> pdb=" O GLU L 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU L 15 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU L 24 " --> pdb=" O GLN L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 44 removed outlier: 3.902A pdb=" N GLU L 35 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS L 39 " --> pdb=" O GLU L 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 134 removed outlier: 3.618A pdb=" N TYR M 133 " --> pdb=" O TRP M 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP M 134 " --> pdb=" O ASN M 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 130 through 134' Processing helix chain 'M' and resid 153 through 158 removed outlier: 3.875A pdb=" N CYS M 158 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 removed outlier: 3.675A pdb=" N ASP M 168 " --> pdb=" O ASP M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 186 through 190 Processing helix chain 'M' and resid 193 through 201 removed outlier: 3.551A pdb=" N GLU M 197 " --> pdb=" O CYS M 193 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA M 199 " --> pdb=" O SER M 195 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE M 200 " --> pdb=" O PHE M 196 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.982A pdb=" N LEU M 224 " --> pdb=" O LEU M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 243 removed outlier: 4.424A pdb=" N GLU M 241 " --> pdb=" O GLN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 283 removed outlier: 3.889A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 283 " --> pdb=" O TRP M 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 277 through 283' Processing helix chain 'M' and resid 332 through 339 removed outlier: 3.725A pdb=" N ALA M 336 " --> pdb=" O GLN M 332 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN M 339 " --> pdb=" O ARG M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 361 removed outlier: 3.709A pdb=" N LEU M 347 " --> pdb=" O ASN M 343 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 removed outlier: 4.238A pdb=" N VAL M 373 " --> pdb=" O ASP M 370 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS M 374 " --> pdb=" O GLN M 371 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE M 375 " --> pdb=" O ARG M 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.479A pdb=" N VAL N 6 " --> pdb=" O ASP N 2 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU N 7 " --> pdb=" O PRO N 3 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN N 9 " --> pdb=" O LEU N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.838A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 removed outlier: 3.657A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 45 Processing helix chain 'N' and resid 73 through 75 No H-bonds generated for 'chain 'N' and resid 73 through 75' Processing helix chain 'N' and resid 76 through 81 removed outlier: 3.570A pdb=" N SER N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 102 removed outlier: 4.664A pdb=" N LEU N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR N 92 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE N 95 " --> pdb=" O ASN N 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 112 removed outlier: 4.158A pdb=" N LYS N 106 " --> pdb=" O ASN N 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.821A pdb=" N THR C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.285A pdb=" N THR G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'K' and resid 170 through 172 removed outlier: 4.001A pdb=" N MET K 172 " --> pdb=" O TYR K 175 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR K 175 " --> pdb=" O MET K 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 234 through 239 removed outlier: 3.601A pdb=" N THR K 277 " --> pdb=" O SER K 235 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE K 237 " --> pdb=" O CYS K 275 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE K 290 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG K 278 " --> pdb=" O LEU K 286 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU K 286 " --> pdb=" O ARG K 278 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3309 1.33 - 1.45: 5533 1.45 - 1.57: 8854 1.57 - 1.69: 580 1.69 - 1.81: 34 Bond restraints: 18310 Sorted by residual: bond pdb=" C LYS K 339 " pdb=" N PRO K 340 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.28e-02 6.10e+03 3.02e+01 bond pdb=" CA THR C 61 " pdb=" C THR C 61 " ideal model delta sigma weight residual 1.524 1.470 0.054 1.26e-02 6.30e+03 1.83e+01 bond pdb=" C ASP K 269 " pdb=" N PRO K 270 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.23e-02 6.61e+03 1.08e+01 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.373 0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" CG ARG F 92 " pdb=" CD ARG F 92 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 ... (remaining 18305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 24330 1.92 - 3.84: 1407 3.84 - 5.76: 144 5.76 - 7.69: 52 7.69 - 9.61: 15 Bond angle restraints: 25948 Sorted by residual: angle pdb=" C ILE F 46 " pdb=" N SER F 47 " pdb=" CA SER F 47 " ideal model delta sigma weight residual 121.54 131.15 -9.61 1.91e+00 2.74e-01 2.53e+01 angle pdb=" CA THR C 61 " pdb=" C THR C 61 " pdb=" O THR C 61 " ideal model delta sigma weight residual 120.70 115.72 4.98 1.03e+00 9.43e-01 2.34e+01 angle pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " ideal model delta sigma weight residual 114.10 122.83 -8.73 2.00e+00 2.50e-01 1.91e+01 angle pdb=" C PHE M 136 " pdb=" CA PHE M 136 " pdb=" CB PHE M 136 " ideal model delta sigma weight residual 110.42 102.18 8.24 1.99e+00 2.53e-01 1.71e+01 angle pdb=" N GLY H 107 " pdb=" CA GLY H 107 " pdb=" C GLY H 107 " ideal model delta sigma weight residual 113.18 122.72 -9.54 2.37e+00 1.78e-01 1.62e+01 ... (remaining 25943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7555 17.89 - 35.79: 1314 35.79 - 53.68: 1171 53.68 - 71.58: 339 71.58 - 89.47: 21 Dihedral angle restraints: 10400 sinusoidal: 6266 harmonic: 4134 Sorted by residual: dihedral pdb=" CA LYS K 398 " pdb=" C LYS K 398 " pdb=" N GLY K 399 " pdb=" CA GLY K 399 " ideal model delta harmonic sigma weight residual -180.00 -136.63 -43.37 0 5.00e+00 4.00e-02 7.52e+01 dihedral pdb=" CA HIS G 38 " pdb=" C HIS G 38 " pdb=" N ALA G 39 " pdb=" CA ALA G 39 " ideal model delta harmonic sigma weight residual 180.00 142.06 37.94 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA PRO K 223 " pdb=" C PRO K 223 " pdb=" N PRO K 224 " pdb=" CA PRO K 224 " ideal model delta harmonic sigma weight residual -180.00 -144.72 -35.28 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 10397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1988 0.050 - 0.100: 727 0.100 - 0.149: 170 0.149 - 0.199: 32 0.199 - 0.249: 7 Chirality restraints: 2924 Sorted by residual: chirality pdb=" CB ILE K 368 " pdb=" CA ILE K 368 " pdb=" CG1 ILE K 368 " pdb=" CG2 ILE K 368 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU E 92 " pdb=" CB LEU E 92 " pdb=" CD1 LEU E 92 " pdb=" CD2 LEU E 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2921 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 336 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO K 337 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO K 337 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 337 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " -0.030 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR F 98 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS G 38 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C HIS G 38 " -0.043 2.00e-02 2.50e+03 pdb=" O HIS G 38 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA G 39 " 0.015 2.00e-02 2.50e+03 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4432 2.81 - 3.33: 15729 3.33 - 3.85: 33369 3.85 - 4.38: 37178 4.38 - 4.90: 52049 Nonbonded interactions: 142757 Sorted by model distance: nonbonded pdb=" OG1 THR C 102 " pdb=" O THR F 96 " model vdw 2.284 3.040 nonbonded pdb=" O LEU N 7 " pdb=" OG1 THR N 10 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.289 3.040 nonbonded pdb=" O ILE C 51 " pdb=" OG1 THR C 54 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR K 185 " pdb=" O LEU K 253 " model vdw 2.301 3.040 ... (remaining 142752 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.020 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 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 : 0.006 0.070 18310 Z= 0.300 Angle : 0.991 9.607 25948 Z= 0.560 Chirality : 0.055 0.249 2924 Planarity : 0.007 0.074 2268 Dihedral : 25.181 89.469 7716 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.72 % Favored : 92.21 % Rotamer: Outliers : 0.80 % Allowed : 5.30 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.18), residues: 1373 helix: -3.19 (0.14), residues: 650 sheet: -2.11 (1.07), residues: 26 loop : -2.69 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 353 HIS 0.015 0.002 HIS B 75 PHE 0.019 0.002 PHE K 271 TYR 0.043 0.003 TYR F 98 ARG 0.009 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.17855 ( 821) hydrogen bonds : angle 7.17455 ( 2079) covalent geometry : bond 0.00623 (18310) covalent geometry : angle 0.99098 (25948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 555 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.8159 (p) cc_final: 0.7953 (p) REVERT: A 51 ILE cc_start: 0.7838 (mm) cc_final: 0.6978 (mm) REVERT: A 59 GLU cc_start: 0.8075 (pm20) cc_final: 0.7853 (pm20) REVERT: A 125 LYS cc_start: 0.8409 (tppt) cc_final: 0.7902 (tppt) REVERT: B 46 ILE cc_start: 0.7029 (mm) cc_final: 0.6718 (mm) REVERT: B 74 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7170 (tm-30) REVERT: D 57 ILE cc_start: 0.7453 (mm) cc_final: 0.6803 (mm) REVERT: D 74 GLU cc_start: 0.7390 (tp30) cc_final: 0.6795 (tp30) REVERT: D 104 ILE cc_start: 0.7635 (tp) cc_final: 0.7253 (tp) REVERT: E 46 VAL cc_start: 0.7292 (p) cc_final: 0.7029 (m) REVERT: E 62 ILE cc_start: 0.6464 (tt) cc_final: 0.5903 (tp) REVERT: E 78 PHE cc_start: 0.8033 (m-10) cc_final: 0.6286 (m-10) REVERT: E 83 ARG cc_start: 0.7128 (tpm170) cc_final: 0.6622 (mmm160) REVERT: F 82 THR cc_start: 0.7622 (t) cc_final: 0.6856 (p) REVERT: G 24 LEU cc_start: 0.8512 (mt) cc_final: 0.7914 (mt) REVERT: G 67 LEU cc_start: 0.7687 (mt) cc_final: 0.6916 (mt) REVERT: H 63 SER cc_start: 0.8015 (t) cc_final: 0.7546 (p) REVERT: H 96 GLU cc_start: 0.7801 (pm20) cc_final: 0.7512 (pm20) REVERT: H 104 ILE cc_start: 0.8453 (tp) cc_final: 0.8238 (tp) REVERT: K 160 GLU cc_start: 0.7539 (pm20) cc_final: 0.6084 (pm20) REVERT: K 167 LEU cc_start: 0.8712 (mm) cc_final: 0.8011 (tp) REVERT: K 197 ILE cc_start: 0.8157 (mm) cc_final: 0.7807 (mm) REVERT: K 236 PHE cc_start: 0.6325 (m-80) cc_final: 0.5511 (m-80) REVERT: K 275 CYS cc_start: 0.7081 (m) cc_final: 0.6278 (t) REVERT: K 276 MET cc_start: 0.5782 (tpt) cc_final: 0.5557 (tpt) REVERT: K 310 GLN cc_start: 0.7077 (pt0) cc_final: 0.6778 (mt0) REVERT: K 350 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7526 (mtt90) REVERT: K 364 HIS cc_start: 0.6767 (t-90) cc_final: 0.6403 (t-90) REVERT: K 372 GLU cc_start: 0.8469 (tt0) cc_final: 0.8008 (tt0) REVERT: M 141 PHE cc_start: 0.7923 (p90) cc_final: 0.7624 (p90) REVERT: M 215 LEU cc_start: 0.4449 (mp) cc_final: 0.3551 (mp) REVERT: M 259 MET cc_start: 0.5054 (pmm) cc_final: 0.4785 (pmm) REVERT: M 265 ILE cc_start: 0.8188 (pt) cc_final: 0.7945 (tp) REVERT: M 278 TYR cc_start: 0.6380 (t80) cc_final: 0.6140 (t80) REVERT: N 23 TYR cc_start: 0.7272 (t80) cc_final: 0.7040 (t80) REVERT: N 97 ILE cc_start: 0.7171 (mt) cc_final: 0.6956 (mt) outliers start: 10 outliers final: 1 residues processed: 557 average time/residue: 0.3648 time to fit residues: 277.7480 Evaluate side-chains 438 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 66 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 GLN L 20 GLN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS N 102 ASN N 107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089183 restraints weight = 58306.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.091655 restraints weight = 30840.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093239 restraints weight = 19421.045| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18310 Z= 0.203 Angle : 0.770 11.125 25948 Z= 0.429 Chirality : 0.043 0.253 2924 Planarity : 0.006 0.052 2268 Dihedral : 29.350 89.657 4818 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.64 % Allowed : 5.54 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1373 helix: -1.74 (0.17), residues: 691 sheet: -2.35 (0.96), residues: 26 loop : -2.54 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 353 HIS 0.010 0.002 HIS M 338 PHE 0.023 0.002 PHE E 54 TYR 0.031 0.002 TYR F 98 ARG 0.011 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.05316 ( 821) hydrogen bonds : angle 4.81755 ( 2079) covalent geometry : bond 0.00442 (18310) covalent geometry : angle 0.77017 (25948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 510 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8146 (mmmt) REVERT: A 93 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7766 (tm-30) REVERT: A 125 LYS cc_start: 0.8508 (tppt) cc_final: 0.8015 (tppt) REVERT: B 37 LEU cc_start: 0.8865 (tp) cc_final: 0.8518 (tp) REVERT: C 63 GLU cc_start: 0.7828 (pp20) cc_final: 0.7482 (tm-30) REVERT: C 84 HIS cc_start: 0.6717 (t-90) cc_final: 0.6129 (t-170) REVERT: D 42 SER cc_start: 0.8604 (m) cc_final: 0.8262 (p) REVERT: D 51 THR cc_start: 0.7903 (p) cc_final: 0.7662 (p) REVERT: D 57 ILE cc_start: 0.7573 (mm) cc_final: 0.7143 (tp) REVERT: D 71 ASP cc_start: 0.7507 (m-30) cc_final: 0.7232 (m-30) REVERT: D 88 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8071 (mmmm) REVERT: D 98 GLN cc_start: 0.7835 (tp40) cc_final: 0.7293 (tp40) REVERT: E 83 ARG cc_start: 0.7509 (tpm170) cc_final: 0.7229 (mmm160) REVERT: F 27 GLN cc_start: 0.7807 (mp-120) cc_final: 0.5942 (mp10) REVERT: F 49 LEU cc_start: 0.7147 (tt) cc_final: 0.6692 (tp) REVERT: F 63 GLU cc_start: 0.7056 (tp30) cc_final: 0.6127 (tp30) REVERT: F 78 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7414 (ptp90) REVERT: F 82 THR cc_start: 0.8049 (t) cc_final: 0.7068 (p) REVERT: F 88 TYR cc_start: 0.6623 (m-10) cc_final: 0.6294 (m-10) REVERT: G 67 LEU cc_start: 0.7695 (mt) cc_final: 0.7207 (mt) REVERT: G 81 THR cc_start: 0.8016 (m) cc_final: 0.7504 (p) REVERT: G 113 ASN cc_start: 0.9044 (t0) cc_final: 0.8806 (t0) REVERT: H 43 TYR cc_start: 0.5314 (m-80) cc_final: 0.5066 (m-10) REVERT: H 63 SER cc_start: 0.8244 (t) cc_final: 0.7651 (p) REVERT: H 65 LEU cc_start: 0.7966 (mm) cc_final: 0.7616 (mm) REVERT: H 74 GLU cc_start: 0.7497 (tp30) cc_final: 0.7264 (tp30) REVERT: K 167 LEU cc_start: 0.8590 (mm) cc_final: 0.8121 (tp) REVERT: K 251 LEU cc_start: 0.8101 (mt) cc_final: 0.7791 (mt) REVERT: K 269 ASP cc_start: 0.8609 (m-30) cc_final: 0.8316 (m-30) REVERT: K 274 TYR cc_start: 0.7404 (m-10) cc_final: 0.7198 (m-10) REVERT: K 364 HIS cc_start: 0.6706 (t-90) cc_final: 0.6393 (t-90) REVERT: K 406 ASN cc_start: 0.6169 (p0) cc_final: 0.5966 (p0) REVERT: L 40 GLU cc_start: 0.7050 (tm-30) cc_final: 0.5741 (tm-30) REVERT: L 44 PHE cc_start: 0.7489 (m-10) cc_final: 0.7076 (m-10) REVERT: M 141 PHE cc_start: 0.8035 (p90) cc_final: 0.7760 (p90) REVERT: M 166 GLU cc_start: 0.8265 (mp0) cc_final: 0.8051 (mp0) REVERT: M 234 LEU cc_start: 0.6843 (mt) cc_final: 0.6630 (mt) REVERT: N 8 GLU cc_start: 0.8324 (mp0) cc_final: 0.7943 (mp0) REVERT: N 31 ASN cc_start: 0.8377 (m110) cc_final: 0.7818 (t0) REVERT: N 96 LEU cc_start: 0.8384 (pp) cc_final: 0.8036 (pp) outliers start: 8 outliers final: 1 residues processed: 513 average time/residue: 0.3598 time to fit residues: 254.1866 Evaluate side-chains 447 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN E 39 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 ASN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.104462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.087672 restraints weight = 57908.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090009 restraints weight = 31354.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091531 restraints weight = 20053.385| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18310 Z= 0.222 Angle : 0.767 11.070 25948 Z= 0.429 Chirality : 0.043 0.196 2924 Planarity : 0.006 0.083 2268 Dihedral : 29.005 89.100 4818 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1373 helix: -1.16 (0.18), residues: 703 sheet: -1.99 (1.10), residues: 26 loop : -2.51 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 353 HIS 0.006 0.001 HIS K 285 PHE 0.023 0.003 PHE K 236 TYR 0.035 0.003 TYR F 98 ARG 0.008 0.001 ARG K 279 Details of bonding type rmsd hydrogen bonds : bond 0.05517 ( 821) hydrogen bonds : angle 4.45428 ( 2079) covalent geometry : bond 0.00496 (18310) covalent geometry : angle 0.76743 (25948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8112 (ttm110) REVERT: A 97 GLU cc_start: 0.7635 (tp30) cc_final: 0.7196 (tp30) REVERT: A 125 LYS cc_start: 0.8666 (tppt) cc_final: 0.8161 (tppt) REVERT: B 37 LEU cc_start: 0.8941 (tp) cc_final: 0.8625 (tp) REVERT: B 59 LYS cc_start: 0.8841 (tppp) cc_final: 0.8564 (tppp) REVERT: C 63 GLU cc_start: 0.7984 (pp20) cc_final: 0.7342 (tm-30) REVERT: C 84 HIS cc_start: 0.7215 (t-90) cc_final: 0.6700 (t-170) REVERT: C 92 ASP cc_start: 0.8446 (t0) cc_final: 0.8218 (t0) REVERT: C 113 ASN cc_start: 0.7922 (p0) cc_final: 0.7604 (p0) REVERT: D 57 ILE cc_start: 0.8428 (mm) cc_final: 0.8224 (tp) REVERT: D 68 PHE cc_start: 0.8476 (t80) cc_final: 0.8275 (t80) REVERT: D 82 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8154 (ttmm) REVERT: D 86 TYR cc_start: 0.8420 (m-10) cc_final: 0.7833 (m-10) REVERT: D 88 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8331 (mtpp) REVERT: D 98 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7738 (tp40) REVERT: E 45 THR cc_start: 0.7881 (p) cc_final: 0.7448 (p) REVERT: E 48 LEU cc_start: 0.8197 (mt) cc_final: 0.7969 (mp) REVERT: E 50 GLU cc_start: 0.7587 (pp20) cc_final: 0.7345 (pp20) REVERT: E 59 GLU cc_start: 0.8201 (tp30) cc_final: 0.7912 (tp30) REVERT: E 70 LEU cc_start: 0.8592 (mm) cc_final: 0.8271 (tp) REVERT: F 82 THR cc_start: 0.8503 (t) cc_final: 0.7773 (p) REVERT: F 88 TYR cc_start: 0.7385 (m-10) cc_final: 0.6912 (m-10) REVERT: G 67 LEU cc_start: 0.8123 (mt) cc_final: 0.7738 (mt) REVERT: G 70 ASN cc_start: 0.7312 (p0) cc_final: 0.7062 (p0) REVERT: G 87 LEU cc_start: 0.7507 (tp) cc_final: 0.7170 (tp) REVERT: G 94 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7028 (mm-30) REVERT: H 65 LEU cc_start: 0.8277 (mm) cc_final: 0.7944 (mm) REVERT: H 74 GLU cc_start: 0.7596 (tp30) cc_final: 0.7245 (tp30) REVERT: H 116 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8302 (mm-30) REVERT: H 118 THR cc_start: 0.8674 (t) cc_final: 0.8437 (p) REVERT: K 176 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7789 (tp30) REVERT: K 310 GLN cc_start: 0.6768 (pp30) cc_final: 0.6543 (pp30) REVERT: K 353 TRP cc_start: 0.8272 (m-90) cc_final: 0.8071 (m-90) REVERT: K 356 THR cc_start: 0.8298 (m) cc_final: 0.8059 (m) REVERT: K 381 THR cc_start: 0.8918 (m) cc_final: 0.8359 (t) REVERT: K 406 ASN cc_start: 0.7080 (p0) cc_final: 0.6850 (p0) REVERT: L 40 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7165 (tp30) REVERT: M 217 PHE cc_start: 0.7248 (t80) cc_final: 0.6958 (t80) REVERT: N 8 GLU cc_start: 0.8327 (mp0) cc_final: 0.7952 (mp0) REVERT: N 31 ASN cc_start: 0.7948 (m110) cc_final: 0.7460 (t0) REVERT: N 97 ILE cc_start: 0.8136 (mt) cc_final: 0.7863 (mt) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.3799 time to fit residues: 270.6407 Evaluate side-chains 460 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 123 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN E 68 GLN F 27 GLN K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.106183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089394 restraints weight = 57772.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091760 restraints weight = 31135.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.093279 restraints weight = 19819.266| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18310 Z= 0.166 Angle : 0.710 11.010 25948 Z= 0.393 Chirality : 0.041 0.176 2924 Planarity : 0.005 0.064 2268 Dihedral : 28.839 88.090 4818 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.21), residues: 1373 helix: -0.86 (0.18), residues: 708 sheet: -2.23 (1.12), residues: 26 loop : -2.32 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 180 HIS 0.005 0.001 HIS M 198 PHE 0.049 0.002 PHE N 21 TYR 0.020 0.002 TYR K 325 ARG 0.010 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 821) hydrogen bonds : angle 4.28228 ( 2079) covalent geometry : bond 0.00367 (18310) covalent geometry : angle 0.71015 (25948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 525 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7561 (m) cc_final: 0.7341 (p) REVERT: A 69 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.7874 (ttp-110) REVERT: A 93 GLN cc_start: 0.8198 (tp40) cc_final: 0.7787 (tm-30) REVERT: A 97 GLU cc_start: 0.7626 (tp30) cc_final: 0.6975 (mm-30) REVERT: A 123 ASP cc_start: 0.7436 (m-30) cc_final: 0.7117 (t0) REVERT: A 125 LYS cc_start: 0.8609 (tppt) cc_final: 0.8250 (tppt) REVERT: A 128 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8121 (mtp85) REVERT: B 37 LEU cc_start: 0.8890 (tp) cc_final: 0.8460 (tp) REVERT: B 59 LYS cc_start: 0.8801 (tppp) cc_final: 0.8591 (tppp) REVERT: B 77 LYS cc_start: 0.8461 (mppt) cc_final: 0.8200 (mmtp) REVERT: C 63 GLU cc_start: 0.7907 (pp20) cc_final: 0.7155 (tm-30) REVERT: C 84 HIS cc_start: 0.7220 (t-90) cc_final: 0.6642 (t-170) REVERT: C 92 ASP cc_start: 0.8424 (t0) cc_final: 0.8188 (t0) REVERT: C 113 ASN cc_start: 0.7832 (p0) cc_final: 0.7592 (p0) REVERT: D 57 ILE cc_start: 0.8285 (mm) cc_final: 0.7929 (tp) REVERT: D 68 PHE cc_start: 0.8475 (t80) cc_final: 0.7616 (t80) REVERT: D 72 ILE cc_start: 0.8483 (tt) cc_final: 0.8220 (tt) REVERT: D 86 TYR cc_start: 0.8167 (m-10) cc_final: 0.6946 (m-10) REVERT: D 88 LYS cc_start: 0.8610 (mmmm) cc_final: 0.8404 (mtpp) REVERT: E 45 THR cc_start: 0.7885 (p) cc_final: 0.7540 (p) REVERT: E 60 LEU cc_start: 0.9042 (pp) cc_final: 0.8138 (pp) REVERT: E 70 LEU cc_start: 0.8474 (mm) cc_final: 0.8039 (tp) REVERT: E 73 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6651 (mt-10) REVERT: E 76 GLN cc_start: 0.7432 (tp-100) cc_final: 0.7100 (tp40) REVERT: F 78 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7782 (ptp90) REVERT: F 88 TYR cc_start: 0.7298 (m-10) cc_final: 0.6827 (m-10) REVERT: G 81 THR cc_start: 0.8421 (m) cc_final: 0.8105 (p) REVERT: G 87 LEU cc_start: 0.7583 (tp) cc_final: 0.6667 (tp) REVERT: H 74 GLU cc_start: 0.7648 (tp30) cc_final: 0.7345 (tp30) REVERT: H 91 THR cc_start: 0.9037 (t) cc_final: 0.8802 (p) REVERT: H 118 THR cc_start: 0.8651 (t) cc_final: 0.8401 (p) REVERT: K 167 LEU cc_start: 0.8650 (mm) cc_final: 0.8201 (tp) REVERT: K 269 ASP cc_start: 0.8458 (m-30) cc_final: 0.8244 (m-30) REVERT: K 356 THR cc_start: 0.8434 (m) cc_final: 0.8152 (m) REVERT: K 381 THR cc_start: 0.8844 (m) cc_final: 0.8377 (t) REVERT: K 406 ASN cc_start: 0.7105 (p0) cc_final: 0.6840 (p0) REVERT: L 40 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6690 (tm-30) REVERT: L 44 PHE cc_start: 0.7499 (m-10) cc_final: 0.6904 (m-10) REVERT: M 209 MET cc_start: 0.5840 (ttp) cc_final: 0.5477 (ttp) REVERT: M 234 LEU cc_start: 0.6830 (mt) cc_final: 0.6614 (mt) REVERT: N 7 LEU cc_start: 0.8390 (pp) cc_final: 0.8146 (pp) REVERT: N 8 GLU cc_start: 0.8361 (mp0) cc_final: 0.7844 (mp0) REVERT: N 89 LEU cc_start: 0.7227 (pp) cc_final: 0.6681 (mt) REVERT: N 97 ILE cc_start: 0.8266 (mt) cc_final: 0.7995 (mt) outliers start: 1 outliers final: 0 residues processed: 525 average time/residue: 0.3763 time to fit residues: 269.8464 Evaluate side-chains 464 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 59 GLN K 310 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.106794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090129 restraints weight = 59356.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092478 restraints weight = 32324.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094008 restraints weight = 20778.504| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18310 Z= 0.164 Angle : 0.709 11.216 25948 Z= 0.393 Chirality : 0.041 0.180 2924 Planarity : 0.005 0.088 2268 Dihedral : 28.671 87.537 4818 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.21), residues: 1373 helix: -0.73 (0.19), residues: 699 sheet: -2.54 (1.08), residues: 26 loop : -2.22 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 353 HIS 0.004 0.001 HIS M 198 PHE 0.041 0.002 PHE K 236 TYR 0.023 0.002 TYR K 325 ARG 0.008 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 821) hydrogen bonds : angle 4.21278 ( 2079) covalent geometry : bond 0.00360 (18310) covalent geometry : angle 0.70872 (25948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 519 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8698 (mm) cc_final: 0.8428 (mt) REVERT: A 69 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7318 (ttp-110) REVERT: A 73 GLU cc_start: 0.7480 (pt0) cc_final: 0.6953 (pt0) REVERT: A 93 GLN cc_start: 0.8096 (tp40) cc_final: 0.7854 (tm-30) REVERT: A 123 ASP cc_start: 0.7593 (m-30) cc_final: 0.7215 (t0) REVERT: A 125 LYS cc_start: 0.8594 (tppt) cc_final: 0.8209 (tppt) REVERT: A 128 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8157 (mtp85) REVERT: C 74 ASP cc_start: 0.7987 (t0) cc_final: 0.7769 (t0) REVERT: D 57 ILE cc_start: 0.8293 (mm) cc_final: 0.8047 (tp) REVERT: D 62 MET cc_start: 0.7986 (ttm) cc_final: 0.7757 (tpp) REVERT: D 71 ASP cc_start: 0.7474 (p0) cc_final: 0.7175 (p0) REVERT: D 72 ILE cc_start: 0.8495 (tt) cc_final: 0.8172 (tt) REVERT: D 74 GLU cc_start: 0.7536 (tp30) cc_final: 0.7301 (tp30) REVERT: D 86 TYR cc_start: 0.8293 (m-10) cc_final: 0.7016 (m-10) REVERT: E 45 THR cc_start: 0.8053 (p) cc_final: 0.7699 (p) REVERT: E 48 LEU cc_start: 0.8324 (mp) cc_final: 0.7784 (mp) REVERT: E 60 LEU cc_start: 0.8528 (pp) cc_final: 0.8261 (pp) REVERT: E 68 GLN cc_start: 0.7684 (tt0) cc_final: 0.7475 (tp-100) REVERT: E 70 LEU cc_start: 0.8503 (mm) cc_final: 0.8276 (tp) REVERT: F 27 GLN cc_start: 0.8062 (pm20) cc_final: 0.7660 (pm20) REVERT: F 36 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7889 (ttm110) REVERT: F 49 LEU cc_start: 0.8176 (tt) cc_final: 0.7968 (tp) REVERT: F 50 ILE cc_start: 0.8629 (tp) cc_final: 0.8390 (tp) REVERT: F 78 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8015 (ptp90) REVERT: F 88 TYR cc_start: 0.7269 (m-10) cc_final: 0.6824 (m-10) REVERT: F 95 ARG cc_start: 0.7581 (ptp-170) cc_final: 0.7152 (ptt-90) REVERT: G 24 LEU cc_start: 0.8321 (mt) cc_final: 0.8117 (mt) REVERT: G 66 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6764 (tm-30) REVERT: G 67 LEU cc_start: 0.8340 (mt) cc_final: 0.8136 (mt) REVERT: G 81 THR cc_start: 0.8488 (m) cc_final: 0.8218 (p) REVERT: G 87 LEU cc_start: 0.7048 (tp) cc_final: 0.6455 (tp) REVERT: G 94 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6940 (mm-30) REVERT: H 74 GLU cc_start: 0.7555 (tp30) cc_final: 0.7236 (tp30) REVERT: K 167 LEU cc_start: 0.8641 (mm) cc_final: 0.8294 (tp) REVERT: K 170 ILE cc_start: 0.8313 (mt) cc_final: 0.7982 (pt) REVERT: K 199 ASP cc_start: 0.7880 (p0) cc_final: 0.7009 (p0) REVERT: K 229 TYR cc_start: 0.5214 (t80) cc_final: 0.3848 (t80) REVERT: K 251 LEU cc_start: 0.8045 (mt) cc_final: 0.7685 (mm) REVERT: K 353 TRP cc_start: 0.8144 (m-90) cc_final: 0.7703 (m-90) REVERT: K 381 THR cc_start: 0.8938 (m) cc_final: 0.8563 (t) REVERT: K 406 ASN cc_start: 0.7284 (p0) cc_final: 0.6992 (p0) REVERT: L 40 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6331 (tm-30) REVERT: L 44 PHE cc_start: 0.7535 (m-10) cc_final: 0.6775 (m-10) REVERT: M 209 MET cc_start: 0.6030 (ttp) cc_final: 0.5718 (ttp) REVERT: N 7 LEU cc_start: 0.8330 (pp) cc_final: 0.7963 (pp) REVERT: N 8 GLU cc_start: 0.8339 (mp0) cc_final: 0.7807 (mp0) REVERT: N 26 GLU cc_start: 0.7782 (tt0) cc_final: 0.7522 (tt0) REVERT: N 89 LEU cc_start: 0.7038 (pp) cc_final: 0.6495 (mt) REVERT: N 97 ILE cc_start: 0.8240 (mt) cc_final: 0.7997 (mt) outliers start: 2 outliers final: 2 residues processed: 520 average time/residue: 0.3769 time to fit residues: 266.8845 Evaluate side-chains 472 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 470 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 0.0030 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN ** K 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.106577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.089948 restraints weight = 59093.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092292 restraints weight = 32204.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093802 restraints weight = 20760.544| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18310 Z= 0.170 Angle : 0.711 11.049 25948 Z= 0.393 Chirality : 0.040 0.249 2924 Planarity : 0.005 0.057 2268 Dihedral : 28.565 87.888 4818 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1373 helix: -0.63 (0.19), residues: 707 sheet: -2.70 (0.98), residues: 26 loop : -2.20 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 353 HIS 0.004 0.001 HIS M 198 PHE 0.035 0.002 PHE K 236 TYR 0.022 0.002 TYR B 72 ARG 0.008 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 821) hydrogen bonds : angle 4.17957 ( 2079) covalent geometry : bond 0.00378 (18310) covalent geometry : angle 0.71089 (25948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6968 (mtp180) REVERT: A 59 GLU cc_start: 0.7960 (pm20) cc_final: 0.7743 (pm20) REVERT: A 69 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.7791 (ttp-110) REVERT: A 106 ASP cc_start: 0.7453 (m-30) cc_final: 0.5708 (m-30) REVERT: A 125 LYS cc_start: 0.8618 (tppt) cc_final: 0.8209 (tppt) REVERT: C 74 ASP cc_start: 0.8087 (t0) cc_final: 0.7817 (t0) REVERT: C 84 HIS cc_start: 0.7514 (t-170) cc_final: 0.7262 (t70) REVERT: D 57 ILE cc_start: 0.8385 (mm) cc_final: 0.8047 (tp) REVERT: D 71 ASP cc_start: 0.7551 (p0) cc_final: 0.7157 (p0) REVERT: D 72 ILE cc_start: 0.8583 (tt) cc_final: 0.8106 (tt) REVERT: D 86 TYR cc_start: 0.8283 (m-10) cc_final: 0.7340 (m-10) REVERT: D 88 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8405 (mtpp) REVERT: E 45 THR cc_start: 0.8210 (p) cc_final: 0.8003 (p) REVERT: E 48 LEU cc_start: 0.8234 (mp) cc_final: 0.7972 (mt) REVERT: E 59 GLU cc_start: 0.7904 (tp30) cc_final: 0.7654 (tp30) REVERT: E 63 ARG cc_start: 0.7755 (tpt90) cc_final: 0.7537 (mmm160) REVERT: E 65 LEU cc_start: 0.8236 (tt) cc_final: 0.7824 (mm) REVERT: E 70 LEU cc_start: 0.8577 (mm) cc_final: 0.8190 (tp) REVERT: E 76 GLN cc_start: 0.7827 (tp40) cc_final: 0.7514 (tp40) REVERT: E 125 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7650 (pttp) REVERT: F 27 GLN cc_start: 0.8033 (pm20) cc_final: 0.7671 (pm20) REVERT: F 49 LEU cc_start: 0.8078 (tt) cc_final: 0.7736 (tp) REVERT: F 50 ILE cc_start: 0.8678 (tp) cc_final: 0.8413 (tp) REVERT: F 78 ARG cc_start: 0.8543 (mtm110) cc_final: 0.8255 (mtm110) REVERT: F 88 TYR cc_start: 0.7209 (m-10) cc_final: 0.6809 (m-10) REVERT: F 95 ARG cc_start: 0.7792 (ptp-170) cc_final: 0.7433 (ptt-90) REVERT: G 30 ARG cc_start: 0.6997 (mtm180) cc_final: 0.6599 (mtp180) REVERT: G 34 TYR cc_start: 0.7960 (m-10) cc_final: 0.7581 (m-10) REVERT: G 66 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 87 LEU cc_start: 0.7022 (tp) cc_final: 0.6572 (tp) REVERT: G 94 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7024 (mm-30) REVERT: H 74 GLU cc_start: 0.7612 (tp30) cc_final: 0.7277 (tp30) REVERT: K 199 ASP cc_start: 0.7751 (p0) cc_final: 0.7193 (p0) REVERT: K 251 LEU cc_start: 0.8336 (mt) cc_final: 0.7970 (mm) REVERT: K 310 GLN cc_start: 0.6868 (pp30) cc_final: 0.6631 (pp30) REVERT: K 316 TYR cc_start: 0.7542 (m-10) cc_final: 0.6749 (m-10) REVERT: K 343 ASP cc_start: 0.6464 (p0) cc_final: 0.6215 (p0) REVERT: K 353 TRP cc_start: 0.8224 (m-90) cc_final: 0.7838 (m-90) REVERT: K 357 LEU cc_start: 0.8140 (mt) cc_final: 0.7856 (mt) REVERT: K 360 LEU cc_start: 0.9185 (tp) cc_final: 0.8876 (tp) REVERT: K 372 GLU cc_start: 0.8000 (tt0) cc_final: 0.7779 (tt0) REVERT: K 406 ASN cc_start: 0.7494 (p0) cc_final: 0.7240 (p0) REVERT: L 40 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7295 (tp30) REVERT: L 44 PHE cc_start: 0.7567 (m-10) cc_final: 0.7346 (m-10) REVERT: M 209 MET cc_start: 0.6123 (ttp) cc_final: 0.5732 (ttp) REVERT: M 234 LEU cc_start: 0.6911 (mt) cc_final: 0.6688 (mt) REVERT: M 278 TYR cc_start: 0.5329 (t80) cc_final: 0.5037 (t80) REVERT: N 7 LEU cc_start: 0.8248 (pp) cc_final: 0.7999 (pp) REVERT: N 8 GLU cc_start: 0.8300 (mp0) cc_final: 0.7795 (mp0) REVERT: N 97 ILE cc_start: 0.8300 (mt) cc_final: 0.8015 (mt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.4002 time to fit residues: 280.5280 Evaluate side-chains 467 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 98 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 HIS N 91 ASN N 102 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.105578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088884 restraints weight = 59182.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091098 restraints weight = 33311.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092510 restraints weight = 22032.578| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18310 Z= 0.219 Angle : 0.764 11.092 25948 Z= 0.422 Chirality : 0.043 0.235 2924 Planarity : 0.005 0.081 2268 Dihedral : 28.539 89.593 4818 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.08 % Allowed : 2.57 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1373 helix: -0.56 (0.19), residues: 700 sheet: -2.80 (0.99), residues: 26 loop : -2.22 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 353 HIS 0.006 0.001 HIS M 198 PHE 0.039 0.002 PHE K 236 TYR 0.025 0.002 TYR F 98 ARG 0.008 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 821) hydrogen bonds : angle 4.30312 ( 2079) covalent geometry : bond 0.00495 (18310) covalent geometry : angle 0.76405 (25948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7284 (mtp180) REVERT: A 69 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8230 (ttp-110) REVERT: A 97 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 106 ASP cc_start: 0.7286 (m-30) cc_final: 0.7030 (m-30) REVERT: A 125 LYS cc_start: 0.8544 (tppt) cc_final: 0.8199 (tppt) REVERT: B 37 LEU cc_start: 0.8742 (tp) cc_final: 0.8517 (tp) REVERT: B 47 SER cc_start: 0.8560 (t) cc_final: 0.8292 (p) REVERT: B 53 GLU cc_start: 0.7600 (pp20) cc_final: 0.7136 (pp20) REVERT: B 88 TYR cc_start: 0.8643 (m-10) cc_final: 0.8296 (m-10) REVERT: C 84 HIS cc_start: 0.7335 (t-170) cc_final: 0.7113 (t70) REVERT: D 57 ILE cc_start: 0.8620 (mm) cc_final: 0.8369 (tp) REVERT: D 71 ASP cc_start: 0.7434 (p0) cc_final: 0.7148 (p0) REVERT: E 56 LYS cc_start: 0.8940 (tttm) cc_final: 0.8319 (tttp) REVERT: E 63 ARG cc_start: 0.7989 (tpt90) cc_final: 0.7770 (mmm160) REVERT: E 76 GLN cc_start: 0.7583 (tp40) cc_final: 0.7309 (tp40) REVERT: E 122 LYS cc_start: 0.8340 (pttm) cc_final: 0.8045 (mtmm) REVERT: E 125 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7385 (pttp) REVERT: F 27 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: F 49 LEU cc_start: 0.8105 (tt) cc_final: 0.7672 (tt) REVERT: F 50 ILE cc_start: 0.8594 (tp) cc_final: 0.8346 (tp) REVERT: F 78 ARG cc_start: 0.8550 (mtm110) cc_final: 0.8002 (ptp90) REVERT: F 88 TYR cc_start: 0.7296 (m-10) cc_final: 0.6762 (m-10) REVERT: F 95 ARG cc_start: 0.8093 (ptp-170) cc_final: 0.7596 (ptp90) REVERT: G 44 ARG cc_start: 0.7004 (tpt90) cc_final: 0.6778 (tpt90) REVERT: G 94 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6965 (mm-30) REVERT: G 113 ASN cc_start: 0.8736 (t0) cc_final: 0.8520 (t0) REVERT: H 37 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7341 (ttpp) REVERT: K 199 ASP cc_start: 0.8051 (p0) cc_final: 0.7493 (p0) REVERT: K 310 GLN cc_start: 0.7116 (pp30) cc_final: 0.6824 (pp30) REVERT: K 323 PHE cc_start: 0.7982 (t80) cc_final: 0.7365 (t80) REVERT: K 343 ASP cc_start: 0.6341 (p0) cc_final: 0.6083 (p0) REVERT: K 353 TRP cc_start: 0.8238 (m-90) cc_final: 0.7929 (m-90) REVERT: K 357 LEU cc_start: 0.8297 (mt) cc_final: 0.8025 (mt) REVERT: K 360 LEU cc_start: 0.9104 (tp) cc_final: 0.8850 (tp) REVERT: K 381 THR cc_start: 0.9083 (m) cc_final: 0.8770 (t) REVERT: K 406 ASN cc_start: 0.7980 (p0) cc_final: 0.7720 (p0) REVERT: M 164 MET cc_start: 0.4600 (mpp) cc_final: 0.3931 (mmp) REVERT: M 209 MET cc_start: 0.6432 (ttp) cc_final: 0.6035 (ttp) REVERT: M 280 ARG cc_start: 0.8144 (mmt180) cc_final: 0.7921 (mpt-90) REVERT: M 353 LYS cc_start: 0.9017 (mptt) cc_final: 0.8736 (mptt) REVERT: N 7 LEU cc_start: 0.8240 (pp) cc_final: 0.8001 (pp) REVERT: N 8 GLU cc_start: 0.8332 (mp0) cc_final: 0.7747 (mp0) outliers start: 1 outliers final: 0 residues processed: 519 average time/residue: 0.3871 time to fit residues: 271.1392 Evaluate side-chains 472 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 128 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS H 87 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 285 HIS K 310 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.106486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089739 restraints weight = 59446.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091949 restraints weight = 33353.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.093371 restraints weight = 22061.432| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18310 Z= 0.183 Angle : 0.746 11.272 25948 Z= 0.409 Chirality : 0.042 0.247 2924 Planarity : 0.005 0.080 2268 Dihedral : 28.529 88.451 4818 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.16 % Allowed : 1.69 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.22), residues: 1373 helix: -0.50 (0.19), residues: 697 sheet: -2.56 (0.98), residues: 26 loop : -2.12 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 247 HIS 0.005 0.001 HIS H 52 PHE 0.036 0.002 PHE K 236 TYR 0.026 0.002 TYR B 72 ARG 0.008 0.001 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 821) hydrogen bonds : angle 4.24350 ( 2079) covalent geometry : bond 0.00414 (18310) covalent geometry : angle 0.74601 (25948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 511 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7481 (mtp180) REVERT: A 58 THR cc_start: 0.8829 (p) cc_final: 0.8351 (t) REVERT: A 69 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.7946 (ttp-110) REVERT: A 93 GLN cc_start: 0.8067 (tp40) cc_final: 0.7824 (tp40) REVERT: A 97 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7278 (mm-30) REVERT: A 125 LYS cc_start: 0.8497 (tppt) cc_final: 0.8227 (tppt) REVERT: B 37 LEU cc_start: 0.8643 (tp) cc_final: 0.8410 (mt) REVERT: B 47 SER cc_start: 0.8510 (t) cc_final: 0.8302 (p) REVERT: B 53 GLU cc_start: 0.7607 (pp20) cc_final: 0.7303 (pp20) REVERT: B 88 TYR cc_start: 0.8592 (m-10) cc_final: 0.8245 (m-10) REVERT: E 74 ILE cc_start: 0.8856 (mm) cc_final: 0.8501 (tp) REVERT: E 76 GLN cc_start: 0.7651 (tp40) cc_final: 0.7367 (tp40) REVERT: E 78 PHE cc_start: 0.8054 (m-10) cc_final: 0.7760 (m-10) REVERT: E 121 LYS cc_start: 0.8720 (tmmt) cc_final: 0.8516 (ttpp) REVERT: E 122 LYS cc_start: 0.8440 (pttm) cc_final: 0.8060 (mtmm) REVERT: E 125 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7998 (pttp) REVERT: F 63 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6556 (tp30) REVERT: F 67 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6683 (mtm-85) REVERT: F 88 TYR cc_start: 0.7408 (m-10) cc_final: 0.6851 (m-10) REVERT: F 95 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7560 (ptp90) REVERT: G 44 ARG cc_start: 0.7039 (tpt90) cc_final: 0.6810 (tpt90) REVERT: G 66 GLU cc_start: 0.7109 (tp30) cc_final: 0.6884 (tp30) REVERT: G 67 LEU cc_start: 0.8269 (mt) cc_final: 0.7995 (mt) REVERT: G 70 ASN cc_start: 0.7695 (p0) cc_final: 0.7427 (p0) REVERT: G 87 LEU cc_start: 0.7234 (tp) cc_final: 0.6968 (tp) REVERT: G 94 GLU cc_start: 0.7600 (mm-30) cc_final: 0.6794 (mm-30) REVERT: G 113 ASN cc_start: 0.8646 (t0) cc_final: 0.8408 (t0) REVERT: H 37 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7339 (ttpp) REVERT: K 199 ASP cc_start: 0.8125 (p0) cc_final: 0.7161 (p0) REVERT: K 221 ARG cc_start: 0.5627 (ttt180) cc_final: 0.4809 (ttt180) REVERT: K 343 ASP cc_start: 0.6278 (p0) cc_final: 0.6020 (p0) REVERT: K 357 LEU cc_start: 0.8342 (mt) cc_final: 0.8096 (mt) REVERT: K 381 THR cc_start: 0.9086 (m) cc_final: 0.8765 (t) REVERT: M 164 MET cc_start: 0.4242 (mpp) cc_final: 0.3740 (mmp) REVERT: M 209 MET cc_start: 0.6262 (ttp) cc_final: 0.5833 (ttp) REVERT: M 249 PHE cc_start: 0.6294 (t80) cc_final: 0.5716 (t80) REVERT: M 254 ASP cc_start: 0.8532 (p0) cc_final: 0.8247 (p0) REVERT: M 353 LYS cc_start: 0.9023 (mptt) cc_final: 0.8748 (mptt) REVERT: N 7 LEU cc_start: 0.8182 (pp) cc_final: 0.7946 (pp) REVERT: N 8 GLU cc_start: 0.8339 (mp0) cc_final: 0.7795 (mp0) REVERT: N 26 GLU cc_start: 0.7759 (tt0) cc_final: 0.7470 (tt0) outliers start: 2 outliers final: 1 residues processed: 511 average time/residue: 0.3804 time to fit residues: 263.5407 Evaluate side-chains 468 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 467 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 0.0010 chunk 131 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 84 HIS C 86 GLN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN N 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.091416 restraints weight = 60303.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093635 restraints weight = 33894.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.095056 restraints weight = 22494.617| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18310 Z= 0.167 Angle : 0.747 12.099 25948 Z= 0.408 Chirality : 0.041 0.260 2924 Planarity : 0.005 0.079 2268 Dihedral : 28.454 87.887 4818 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.22), residues: 1373 helix: -0.45 (0.19), residues: 691 sheet: -2.60 (0.91), residues: 26 loop : -2.12 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 247 HIS 0.005 0.001 HIS M 198 PHE 0.037 0.002 PHE K 236 TYR 0.025 0.002 TYR F 72 ARG 0.014 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 821) hydrogen bonds : angle 4.28244 ( 2079) covalent geometry : bond 0.00370 (18310) covalent geometry : angle 0.74733 (25948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7430 (mtp180) REVERT: A 57 SER cc_start: 0.8102 (p) cc_final: 0.7892 (p) REVERT: A 58 THR cc_start: 0.8836 (p) cc_final: 0.8470 (t) REVERT: A 69 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.7863 (ttp-110) REVERT: A 93 GLN cc_start: 0.7980 (tp40) cc_final: 0.7700 (tp40) REVERT: A 97 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 125 LYS cc_start: 0.8448 (tppt) cc_final: 0.8189 (tppt) REVERT: B 37 LEU cc_start: 0.8642 (tp) cc_final: 0.8144 (tp) REVERT: B 44 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8160 (ptpt) REVERT: B 53 GLU cc_start: 0.7571 (pp20) cc_final: 0.7371 (pp20) REVERT: D 86 TYR cc_start: 0.8308 (m-10) cc_final: 0.7240 (m-10) REVERT: E 71 VAL cc_start: 0.8845 (m) cc_final: 0.8553 (m) REVERT: E 74 ILE cc_start: 0.8700 (mm) cc_final: 0.7785 (tp) REVERT: E 76 GLN cc_start: 0.7506 (tp40) cc_final: 0.7226 (tp40) REVERT: E 121 LYS cc_start: 0.8621 (tmmt) cc_final: 0.8341 (ttpp) REVERT: F 49 LEU cc_start: 0.7941 (tp) cc_final: 0.7703 (tp) REVERT: F 59 LYS cc_start: 0.8636 (tppt) cc_final: 0.7621 (tppt) REVERT: F 63 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6628 (mm-30) REVERT: F 67 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6752 (mtm-85) REVERT: F 88 TYR cc_start: 0.7485 (m-10) cc_final: 0.6962 (m-10) REVERT: F 95 ARG cc_start: 0.8161 (ptp-170) cc_final: 0.7885 (ptp90) REVERT: H 88 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8467 (ttmm) REVERT: H 98 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7288 (tp40) REVERT: K 199 ASP cc_start: 0.7975 (p0) cc_final: 0.7674 (p0) REVERT: K 216 LYS cc_start: 0.7923 (pttm) cc_final: 0.7698 (pttm) REVERT: K 343 ASP cc_start: 0.6265 (p0) cc_final: 0.6030 (p0) REVERT: K 357 LEU cc_start: 0.8312 (mt) cc_final: 0.8037 (mt) REVERT: M 209 MET cc_start: 0.6182 (ttp) cc_final: 0.5839 (ttp) REVERT: M 249 PHE cc_start: 0.6280 (t80) cc_final: 0.5626 (t80) REVERT: M 254 ASP cc_start: 0.8436 (p0) cc_final: 0.8189 (p0) REVERT: M 353 LYS cc_start: 0.9024 (mptt) cc_final: 0.8732 (mptt) REVERT: N 8 GLU cc_start: 0.8323 (mp0) cc_final: 0.7763 (mp0) REVERT: N 26 GLU cc_start: 0.7732 (tt0) cc_final: 0.7530 (tt0) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3898 time to fit residues: 266.9356 Evaluate side-chains 458 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 94 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN N 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091552 restraints weight = 59825.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093561 restraints weight = 35056.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094868 restraints weight = 24047.925| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.8087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18310 Z= 0.175 Angle : 0.742 10.868 25948 Z= 0.408 Chirality : 0.041 0.262 2924 Planarity : 0.006 0.081 2268 Dihedral : 28.399 87.890 4818 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1373 helix: -0.36 (0.19), residues: 683 sheet: -2.48 (0.91), residues: 26 loop : -2.05 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 247 HIS 0.006 0.001 HIS F 75 PHE 0.036 0.002 PHE K 236 TYR 0.026 0.002 TYR C 52 ARG 0.015 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 821) hydrogen bonds : angle 4.28679 ( 2079) covalent geometry : bond 0.00391 (18310) covalent geometry : angle 0.74213 (25948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7697 (ttp80) REVERT: A 57 SER cc_start: 0.8529 (p) cc_final: 0.7703 (p) REVERT: A 58 THR cc_start: 0.8808 (p) cc_final: 0.8509 (t) REVERT: A 69 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.7942 (ttp-110) REVERT: A 97 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7129 (mm-30) REVERT: A 125 LYS cc_start: 0.8376 (tppt) cc_final: 0.8176 (tppt) REVERT: B 37 LEU cc_start: 0.8665 (tp) cc_final: 0.8383 (mt) REVERT: B 44 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8279 (ptpt) REVERT: C 31 ILE cc_start: 0.8789 (mm) cc_final: 0.7740 (mt) REVERT: C 44 ARG cc_start: 0.7171 (pmt-80) cc_final: 0.6833 (pmt-80) REVERT: D 74 GLU cc_start: 0.7398 (tp30) cc_final: 0.7198 (tp30) REVERT: D 86 TYR cc_start: 0.8338 (m-10) cc_final: 0.7188 (m-10) REVERT: E 73 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6548 (mm-30) REVERT: E 74 ILE cc_start: 0.8638 (mm) cc_final: 0.8193 (tp) REVERT: E 76 GLN cc_start: 0.7448 (tp40) cc_final: 0.7204 (tp40) REVERT: E 125 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8101 (mtmt) REVERT: F 50 ILE cc_start: 0.8725 (tp) cc_final: 0.8456 (tp) REVERT: F 59 LYS cc_start: 0.8648 (tppt) cc_final: 0.7938 (tppt) REVERT: F 63 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6978 (mm-30) REVERT: F 67 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: F 88 TYR cc_start: 0.7342 (m-10) cc_final: 0.6794 (m-10) REVERT: F 95 ARG cc_start: 0.8204 (ptp-170) cc_final: 0.7865 (ptp90) REVERT: G 52 TYR cc_start: 0.7083 (t80) cc_final: 0.6803 (t80) REVERT: G 66 GLU cc_start: 0.7067 (tp30) cc_final: 0.6832 (tm-30) REVERT: G 67 LEU cc_start: 0.8275 (mt) cc_final: 0.8021 (mt) REVERT: G 87 LEU cc_start: 0.7111 (tp) cc_final: 0.6419 (tp) REVERT: H 37 LYS cc_start: 0.7460 (ttpp) cc_final: 0.7121 (ttpp) REVERT: H 88 LYS cc_start: 0.8683 (ptpp) cc_final: 0.8467 (ttmm) REVERT: K 216 LYS cc_start: 0.7998 (pttm) cc_final: 0.7732 (pttm) REVERT: K 238 GLU cc_start: 0.7596 (pt0) cc_final: 0.7386 (pt0) REVERT: K 343 ASP cc_start: 0.6187 (p0) cc_final: 0.5900 (p0) REVERT: M 209 MET cc_start: 0.6236 (ttp) cc_final: 0.5920 (ttp) REVERT: M 249 PHE cc_start: 0.6297 (t80) cc_final: 0.5616 (t80) REVERT: M 353 LYS cc_start: 0.8999 (mptt) cc_final: 0.8684 (mptt) REVERT: M 355 GLU cc_start: 0.7673 (pt0) cc_final: 0.6978 (pt0) REVERT: N 8 GLU cc_start: 0.8308 (mp0) cc_final: 0.7808 (mp0) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3992 time to fit residues: 267.0707 Evaluate side-chains 450 residues out of total 1246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 0.9990 chunk 95 optimal weight: 0.0030 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.0170 chunk 91 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 HIS ** K 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093154 restraints weight = 59655.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095215 restraints weight = 34861.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096527 restraints weight = 23692.966| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.8327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18310 Z= 0.165 Angle : 0.757 13.138 25948 Z= 0.412 Chirality : 0.041 0.282 2924 Planarity : 0.005 0.061 2268 Dihedral : 28.373 88.784 4818 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1373 helix: -0.39 (0.19), residues: 687 sheet: -2.38 (0.91), residues: 26 loop : -1.95 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 247 HIS 0.007 0.001 HIS F 75 PHE 0.040 0.002 PHE K 236 TYR 0.039 0.002 TYR B 88 ARG 0.015 0.001 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 821) hydrogen bonds : angle 4.33874 ( 2079) covalent geometry : bond 0.00362 (18310) covalent geometry : angle 0.75727 (25948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6777.34 seconds wall clock time: 118 minutes 40.52 seconds (7120.52 seconds total)