Starting phenix.real_space_refine on Fri Jul 3 04:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g5o_29751/07_2026/8g5o_29751.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 47 5.16 5 C 7308 2.51 5 N 2199 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11952 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7219 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 1962 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 353} Link IDs: {'PTRANS': 18, 'TRANS': 378} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1324 Unresolved non-hydrogen angles: 1700 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLU:plan': 25, 'GLN:plan1': 14, 'ARG:plan': 23, 'HIS:plan': 15, 'PHE:plan': 17, 'ASP:plan': 18, 'ASN:plan1': 18, 'TRP:plan': 10, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 723 Chain: "C" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 1974 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 356} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1331 Unresolved non-hydrogen angles: 1710 Unresolved non-hydrogen dihedrals: 1136 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLU:plan': 28, 'GLN:plan1': 15, 'ARG:plan': 22, 'HIS:plan': 15, 'PHE:plan': 17, 'ASP:plan': 17, 'ASN:plan1': 17, 'TRP:plan': 10, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 728 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 12, 'rna3p': 4} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 2.55, per 1000 atoms: 0.21 Number of scatterers: 11952 At special positions: 0 Unit cell: (104.851, 101.549, 140.352, 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 47 16.00 P 38 15.00 O 2360 8.00 N 2199 7.00 C 7308 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: 0.76 Conformation dependent library (CDL) restraints added in 508.3 milliseconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 11 sheets defined 38.2% alpha, 12.1% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.854A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.687A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.660A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.938A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 470 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 541 through 551 removed outlier: 3.654A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.543A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.708A pdb=" N GLU A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 removed outlier: 3.772A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 5.187A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.811A pdb=" N ARG A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 982 through 988 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.750A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.630A pdb=" N TYR A1221 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 200 removed outlier: 4.360A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.559A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.695A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 4.027A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.310A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.932A pdb=" N LEU C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.705A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 266 removed outlier: 4.521A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.014A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.714A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA A 212 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.504A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.785A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.868A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.986A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.704A pdb=" N LYS C 134 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 207 through 218 removed outlier: 6.633A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.981A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 462 " --> pdb=" O SER C 457 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.00 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: 2347 1.33 - 1.45: 3034 1.45 - 1.57: 6698 1.57 - 1.69: 77 1.69 - 1.81: 77 Bond restraints: 12233 Sorted by residual: bond pdb=" CG PRO A1203 " pdb=" CD PRO A1203 " ideal model delta sigma weight residual 1.503 1.267 0.236 3.40e-02 8.65e+02 4.81e+01 bond pdb=" C1' DC T 10 " pdb=" N1 DC T 10 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N THR A 586 " pdb=" CA THR A 586 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" C1' DT T 7 " pdb=" N1 DT T 7 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" N THR A1199 " pdb=" CA THR A1199 " ideal model delta sigma weight residual 1.462 1.491 -0.028 7.70e-03 1.69e+04 1.36e+01 ... (remaining 12228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 16763 3.81 - 7.62: 140 7.62 - 11.42: 7 11.42 - 15.23: 1 15.23 - 19.04: 2 Bond angle restraints: 16913 Sorted by residual: angle pdb=" N PRO A1203 " pdb=" CD PRO A1203 " pdb=" CG PRO A1203 " ideal model delta sigma weight residual 103.20 85.11 18.09 1.50e+00 4.44e-01 1.45e+02 angle pdb=" CA PRO A1203 " pdb=" CB PRO A1203 " pdb=" CG PRO A1203 " ideal model delta sigma weight residual 104.50 85.46 19.04 1.90e+00 2.77e-01 1.00e+02 angle pdb=" CA PRO A 867 " pdb=" N PRO A 867 " pdb=" CD PRO A 867 " ideal model delta sigma weight residual 112.00 98.43 13.57 1.40e+00 5.10e-01 9.40e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.33 110.43 -7.10 9.30e-01 1.16e+00 5.83e+01 angle pdb=" N PRO A 340 " pdb=" CA PRO A 340 " pdb=" CB PRO A 340 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 ... (remaining 16908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.47: 6920 32.47 - 64.94: 263 64.94 - 97.41: 22 97.41 - 129.87: 0 129.87 - 162.34: 1 Dihedral angle restraints: 7206 sinusoidal: 2280 harmonic: 4926 Sorted by residual: dihedral pdb=" CD ARG A 927 " pdb=" NE ARG A 927 " pdb=" CZ ARG A 927 " pdb=" NH1 ARG A 927 " ideal model delta sinusoidal sigma weight residual 0.00 -82.49 82.49 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CD ARG A 140 " pdb=" NE ARG A 140 " pdb=" CZ ARG A 140 " pdb=" NH1 ARG A 140 " ideal model delta sinusoidal sigma weight residual 0.00 -42.47 42.47 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA ASN A 438 " pdb=" C ASN A 438 " pdb=" N GLN A 439 " pdb=" CA GLN A 439 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 7203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1504 0.043 - 0.086: 307 0.086 - 0.129: 151 0.129 - 0.172: 24 0.172 - 0.215: 5 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA PRO A 340 " pdb=" N PRO A 340 " pdb=" C PRO A 340 " pdb=" CB PRO A 340 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PRO A 625 " pdb=" N PRO A 625 " pdb=" C PRO A 625 " pdb=" CB PRO A 625 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE B 156 " pdb=" N ILE B 156 " pdb=" C ILE B 156 " pdb=" CB ILE B 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 1988 not shown) Planarity restraints: 2137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 927 " -1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A 927 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 927 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 927 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 927 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 140 " -0.721 9.50e-02 1.11e+02 3.23e-01 6.36e+01 pdb=" NE ARG A 140 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 140 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 140 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 140 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 866 " 0.087 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO A 867 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 867 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 867 " 0.065 5.00e-02 4.00e+02 ... (remaining 2134 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 117 2.58 - 3.16: 10164 3.16 - 3.74: 18634 3.74 - 4.32: 22907 4.32 - 4.90: 38160 Nonbonded interactions: 89982 Sorted by model distance: nonbonded pdb=" OG1 THR A 989 " pdb=" OE1 GLU A1056 " model vdw 2.003 3.040 nonbonded pdb=" O HIS A 805 " pdb=" OG SER A 809 " model vdw 2.018 3.040 nonbonded pdb=" OD1 ASP A 904 " pdb=" N ALA A 905 " model vdw 2.042 3.120 nonbonded pdb=" OG SER A 237 " pdb=" OG SER A 240 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.067 3.040 ... (remaining 89977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 68 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 219 or resid 229 through 355 or \ resid 368 through 485)) selection = (chain 'C' and (resid 68 through 160 or resid 169 through 219 or resid 229 throu \ gh 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 11.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5294 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 : 0.005 0.236 12233 Z= 0.311 Angle : 0.851 19.038 16913 Z= 0.523 Chirality : 0.046 0.215 1991 Planarity : 0.014 0.489 2137 Dihedral : 16.464 162.343 4012 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.72 % Allowed : 22.06 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.22), residues: 1690 helix: 1.96 (0.23), residues: 655 sheet: 0.96 (0.37), residues: 217 loop : -1.66 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 457 TYR 0.011 0.001 TYR A 831 PHE 0.012 0.001 PHE A 770 TRP 0.027 0.001 TRP A 486 HIS 0.006 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.31 (12233) covalent geometry : angle 0.85105 / 0.52 (16913) hydrogen bonds : bond 0.11988 / 8.34 ( 593) hydrogen bonds : angle 5.18467 / 3.59 ( 1660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.279 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 133 average time/residue: 0.4640 time to fit residues: 67.7359 Evaluate side-chains 104 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 1203 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 285 GLN A 565 HIS A 754 HIS A 803 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A 976 GLN A1175 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.196978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.144270 restraints weight = 22880.042| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 4.79 r_work: 0.3904 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12233 Z= 0.247 Angle : 0.694 7.722 16913 Z= 0.370 Chirality : 0.046 0.218 1991 Planarity : 0.006 0.088 2137 Dihedral : 15.226 169.596 2297 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 6.74 % Allowed : 19.82 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1690 helix: 1.52 (0.21), residues: 661 sheet: 0.97 (0.37), residues: 221 loop : -1.79 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 597 TYR 0.021 0.002 TYR A1108 PHE 0.026 0.002 PHE A 197 TRP 0.024 0.002 TRP A 484 HIS 0.007 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (12233) covalent geometry : angle 0.69355 / 0.37 (16913) hydrogen bonds : bond 0.04411 / 2.92 ( 593) hydrogen bonds : angle 4.28018 / 2.98 ( 1660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 0.412 Fit side-chains TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 78 MET cc_start: 0.8330 (mtt) cc_final: 0.8050 (mtt) REVERT: A 146 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: A 447 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: A 612 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5601 (tm) REVERT: A 793 GLU cc_start: 0.7443 (tt0) cc_final: 0.7237 (tt0) REVERT: A 866 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.7004 (ttp80) REVERT: A 968 GLN cc_start: 0.7568 (mt0) cc_final: 0.7362 (mt0) REVERT: A 1198 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6178 (tmtt) outliers start: 51 outliers final: 18 residues processed: 137 average time/residue: 0.3763 time to fit residues: 57.5527 Evaluate side-chains 120 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 32 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 40.0000 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 131 optimal weight: 50.0000 chunk 77 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.200466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.150296 restraints weight = 22954.271| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 4.60 r_work: 0.3983 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12233 Z= 0.130 Angle : 0.588 8.090 16913 Z= 0.309 Chirality : 0.042 0.205 1991 Planarity : 0.004 0.074 2137 Dihedral : 15.047 166.145 2292 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.89 % Allowed : 22.06 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.21), residues: 1690 helix: 1.79 (0.22), residues: 659 sheet: 1.14 (0.37), residues: 207 loop : -1.70 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.031 0.001 TYR A 178 PHE 0.016 0.001 PHE A 610 TRP 0.018 0.001 TRP A 486 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12233) covalent geometry : angle 0.58783 / 0.31 (16913) hydrogen bonds : bond 0.03395 / 2.26 ( 593) hydrogen bonds : angle 3.89189 / 2.71 ( 1660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.286 Fit side-chains TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 115 GLN cc_start: 0.9063 (tp-100) cc_final: 0.8684 (tm-30) REVERT: A 146 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: A 228 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.4275 (mt) REVERT: A 355 SER cc_start: 0.7866 (m) cc_final: 0.7415 (p) REVERT: A 447 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: A 612 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5405 (tm) REVERT: A 779 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6442 (tm) REVERT: A 968 GLN cc_start: 0.7476 (mt0) cc_final: 0.7161 (mt0) outliers start: 37 outliers final: 14 residues processed: 128 average time/residue: 0.3741 time to fit residues: 53.4780 Evaluate side-chains 115 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 110 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.199395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.148055 restraints weight = 22831.404| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 5.01 r_work: 0.3959 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 12233 Z= 0.146 Angle : 0.579 6.933 16913 Z= 0.306 Chirality : 0.042 0.190 1991 Planarity : 0.004 0.072 2137 Dihedral : 15.032 166.605 2292 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 6.21 % Allowed : 21.66 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1690 helix: 1.69 (0.21), residues: 672 sheet: 1.14 (0.37), residues: 208 loop : -1.80 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 101 TYR 0.018 0.001 TYR A 178 PHE 0.013 0.001 PHE A 197 TRP 0.019 0.001 TRP A 486 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (12233) covalent geometry : angle 0.57932 / 0.31 (16913) hydrogen bonds : bond 0.03319 / 2.18 ( 593) hydrogen bonds : angle 3.80927 / 2.65 ( 1660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: A 295 MET cc_start: 0.8159 (mtt) cc_final: 0.7551 (mtp) REVERT: A 355 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 363 TYR cc_start: 0.6388 (m-80) cc_final: 0.6114 (m-10) REVERT: A 447 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 612 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5444 (tm) REVERT: A 968 GLN cc_start: 0.7497 (mt0) cc_final: 0.7170 (mt0) REVERT: A 1068 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5799 (p0) REVERT: A 1071 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5844 (mtm110) REVERT: A 1198 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5661 (tmtt) outliers start: 47 outliers final: 23 residues processed: 135 average time/residue: 0.3936 time to fit residues: 59.5311 Evaluate side-chains 128 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1071 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 8 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 chunk 85 optimal weight: 0.0980 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 803 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.200335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.150622 restraints weight = 22846.651| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 5.05 r_work: 0.3980 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12233 Z= 0.126 Angle : 0.570 8.166 16913 Z= 0.298 Chirality : 0.042 0.203 1991 Planarity : 0.004 0.068 2137 Dihedral : 14.990 165.764 2292 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.34 % Allowed : 22.06 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1690 helix: 1.77 (0.22), residues: 673 sheet: 1.14 (0.37), residues: 208 loop : -1.80 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 101 TYR 0.018 0.001 TYR A1210 PHE 0.010 0.001 PHE A 949 TRP 0.020 0.001 TRP A 486 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (12233) covalent geometry : angle 0.56991 / 0.30 (16913) hydrogen bonds : bond 0.03051 / 2.00 ( 593) hydrogen bonds : angle 3.68024 / 2.57 ( 1660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: A 295 MET cc_start: 0.8125 (mtt) cc_final: 0.7837 (mtp) REVERT: A 355 SER cc_start: 0.7867 (m) cc_final: 0.7444 (p) REVERT: A 363 TYR cc_start: 0.6395 (m-80) cc_final: 0.6118 (m-10) REVERT: A 447 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 612 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5428 (tm) REVERT: A 968 GLN cc_start: 0.7567 (mt0) cc_final: 0.7239 (mt0) REVERT: A 1198 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5943 (tmtt) outliers start: 48 outliers final: 17 residues processed: 133 average time/residue: 0.3652 time to fit residues: 54.5651 Evaluate side-chains 117 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 104 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 277 HIS ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.138280 restraints weight = 23131.575| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 4.56 r_work: 0.3829 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 12233 Z= 0.348 Angle : 0.751 8.157 16913 Z= 0.402 Chirality : 0.049 0.255 1991 Planarity : 0.006 0.094 2137 Dihedral : 15.239 167.839 2292 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 7.93 % Allowed : 22.46 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1690 helix: 1.16 (0.21), residues: 665 sheet: 1.30 (0.38), residues: 195 loop : -2.10 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 101 TYR 0.019 0.003 TYR A 282 PHE 0.026 0.002 PHE A 88 TRP 0.022 0.003 TRP A 748 HIS 0.008 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.35 (12233) covalent geometry : angle 0.75051 / 0.40 (16913) hydrogen bonds : bond 0.04669 / 3.07 ( 593) hydrogen bonds : angle 4.37422 / 3.05 ( 1660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 103 time to evaluate : 0.331 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7869 (p) REVERT: A 447 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: A 910 MET cc_start: 0.6479 (mpp) cc_final: 0.5517 (mmm) REVERT: A 968 GLN cc_start: 0.7575 (mt0) cc_final: 0.7221 (mt0) REVERT: A 1054 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: A 1198 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5877 (tmtt) outliers start: 60 outliers final: 31 residues processed: 144 average time/residue: 0.3681 time to fit residues: 59.5099 Evaluate side-chains 132 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 169 optimal weight: 30.0000 chunk 140 optimal weight: 50.0000 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.193660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.136491 restraints weight = 23010.010| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.85 r_work: 0.3871 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 12233 Z= 0.279 Angle : 0.710 12.135 16913 Z= 0.376 Chirality : 0.046 0.198 1991 Planarity : 0.006 0.091 2137 Dihedral : 15.233 165.767 2292 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 7.66 % Allowed : 22.85 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1690 helix: 1.21 (0.21), residues: 665 sheet: 0.96 (0.36), residues: 215 loop : -2.18 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 101 TYR 0.038 0.003 TYR A 178 PHE 0.019 0.002 PHE A 197 TRP 0.026 0.002 TRP A 486 HIS 0.006 0.002 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.28 (12233) covalent geometry : angle 0.71049 / 0.38 (16913) hydrogen bonds : bond 0.04188 / 2.76 ( 593) hydrogen bonds : angle 4.30355 / 3.00 ( 1660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 100 time to evaluate : 0.383 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: A 355 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (p) REVERT: A 363 TYR cc_start: 0.6434 (m-80) cc_final: 0.6166 (m-10) REVERT: A 447 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: A 466 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8294 (tm) REVERT: A 612 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.5390 (tm) REVERT: A 866 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6924 (ttp80) REVERT: A 910 MET cc_start: 0.6438 (mpp) cc_final: 0.5450 (mmm) REVERT: A 968 GLN cc_start: 0.7493 (mt0) cc_final: 0.7134 (mt0) REVERT: A 973 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 1054 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 1198 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.6095 (tmtt) outliers start: 58 outliers final: 32 residues processed: 141 average time/residue: 0.4175 time to fit residues: 66.1127 Evaluate side-chains 136 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1197 CYS Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 129 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 146 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 120 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 116 optimal weight: 50.0000 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 440 ASN A 472 GLN ** A 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.193920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.140471 restraints weight = 22669.282| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 4.42 r_work: 0.3896 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 12233 Z= 0.221 Angle : 0.673 10.603 16913 Z= 0.353 Chirality : 0.045 0.189 1991 Planarity : 0.005 0.084 2137 Dihedral : 15.212 164.766 2292 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 6.61 % Allowed : 24.70 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1690 helix: 1.38 (0.21), residues: 666 sheet: 1.17 (0.37), residues: 204 loop : -2.17 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 101 TYR 0.027 0.002 TYR A 178 PHE 0.015 0.002 PHE A 197 TRP 0.027 0.002 TRP A 486 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (12233) covalent geometry : angle 0.67313 / 0.35 (16913) hydrogen bonds : bond 0.03835 / 2.52 ( 593) hydrogen bonds : angle 4.16706 / 2.90 ( 1660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 0.455 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: A 355 SER cc_start: 0.8104 (OUTLIER) cc_final: 0.7885 (p) REVERT: A 363 TYR cc_start: 0.6400 (m-80) cc_final: 0.6088 (m-10) REVERT: A 439 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: A 447 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 466 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8294 (tm) REVERT: A 612 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5483 (tm) REVERT: A 968 GLN cc_start: 0.7469 (mt0) cc_final: 0.7114 (mt0) REVERT: A 1054 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 1198 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5958 (tmtt) outliers start: 50 outliers final: 30 residues processed: 134 average time/residue: 0.4339 time to fit residues: 64.9882 Evaluate side-chains 132 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1054 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 156 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 78 optimal weight: 0.0570 chunk 172 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 126 optimal weight: 40.0000 chunk 31 optimal weight: 0.0370 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 472 GLN ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.198930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.143856 restraints weight = 22879.540| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 3.82 r_work: 0.3978 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 12233 Z= 0.129 Angle : 0.624 8.948 16913 Z= 0.325 Chirality : 0.043 0.227 1991 Planarity : 0.004 0.065 2137 Dihedral : 15.102 163.665 2292 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.96 % Allowed : 27.34 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1690 helix: 1.53 (0.21), residues: 676 sheet: 1.10 (0.38), residues: 199 loop : -1.95 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.021 0.002 TYR A 178 PHE 0.015 0.001 PHE A1058 TRP 0.031 0.002 TRP A 486 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12233) covalent geometry : angle 0.62356 / 0.32 (16913) hydrogen bonds : bond 0.03018 / 2.00 ( 593) hydrogen bonds : angle 3.81240 / 2.66 ( 1660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.455 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8844 (p0) cc_final: 0.8424 (m-30) REVERT: A 146 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: A 355 SER cc_start: 0.7658 (m) cc_final: 0.7250 (p) REVERT: A 363 TYR cc_start: 0.6365 (m-80) cc_final: 0.6039 (m-10) REVERT: A 439 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: A 447 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 466 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8314 (tm) REVERT: A 612 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5354 (tm) REVERT: A 614 TYR cc_start: 0.8384 (m-10) cc_final: 0.8181 (m-10) REVERT: A 793 GLU cc_start: 0.7301 (tt0) cc_final: 0.6743 (tm-30) REVERT: A 910 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.4634 (mmm) REVERT: A 968 GLN cc_start: 0.7460 (mt0) cc_final: 0.7145 (mt0) REVERT: A 1054 GLU cc_start: 0.7729 (tp30) cc_final: 0.7189 (mp0) outliers start: 30 outliers final: 15 residues processed: 127 average time/residue: 0.4441 time to fit residues: 62.8570 Evaluate side-chains 119 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 141 optimal weight: 50.0000 chunk 162 optimal weight: 5.9990 chunk 116 optimal weight: 50.0000 chunk 159 optimal weight: 40.0000 chunk 2 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 147 optimal weight: 0.0270 chunk 47 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.195680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.143859 restraints weight = 22703.218| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 4.72 r_work: 0.3887 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 12233 Z= 0.180 Angle : 0.651 12.092 16913 Z= 0.337 Chirality : 0.044 0.198 1991 Planarity : 0.005 0.068 2137 Dihedral : 15.125 165.765 2292 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.10 % Allowed : 28.40 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1690 helix: 1.55 (0.21), residues: 671 sheet: 1.18 (0.38), residues: 195 loop : -2.00 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1208 TYR 0.023 0.002 TYR A 178 PHE 0.014 0.001 PHE A 197 TRP 0.030 0.002 TRP A 486 HIS 0.004 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (12233) covalent geometry : angle 0.65107 / 0.34 (16913) hydrogen bonds : bond 0.03348 / 2.22 ( 593) hydrogen bonds : angle 3.86255 / 2.70 ( 1660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.434 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8956 (p0) cc_final: 0.8422 (m-30) REVERT: A 146 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: A 355 SER cc_start: 0.7786 (m) cc_final: 0.7344 (p) REVERT: A 363 TYR cc_start: 0.6368 (m-80) cc_final: 0.6159 (m-10) REVERT: A 439 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: A 447 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 466 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8343 (tm) REVERT: A 594 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.5293 (mp) REVERT: A 612 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5369 (tm) REVERT: A 910 MET cc_start: 0.6273 (mtt) cc_final: 0.4673 (mmm) REVERT: A 968 GLN cc_start: 0.7491 (mt0) cc_final: 0.7140 (mt0) REVERT: A 1054 GLU cc_start: 0.7865 (tp30) cc_final: 0.7318 (mp0) outliers start: 31 outliers final: 18 residues processed: 125 average time/residue: 0.4334 time to fit residues: 60.4863 Evaluate side-chains 121 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 45 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 37 optimal weight: 0.0030 chunk 86 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 115 optimal weight: 50.0000 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 971 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.198795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.148452 restraints weight = 23007.180| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 4.53 r_work: 0.3985 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12233 Z= 0.121 Angle : 0.627 11.593 16913 Z= 0.324 Chirality : 0.043 0.235 1991 Planarity : 0.004 0.057 2137 Dihedral : 15.049 164.855 2292 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.30 % Allowed : 29.19 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1690 helix: 1.63 (0.21), residues: 676 sheet: 1.08 (0.38), residues: 199 loop : -1.89 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.018 0.001 TYR A 178 PHE 0.021 0.001 PHE A 749 TRP 0.032 0.002 TRP A 486 HIS 0.003 0.001 HIS A 828 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12233) covalent geometry : angle 0.62729 / 0.32 (16913) hydrogen bonds : bond 0.02862 / 1.91 ( 593) hydrogen bonds : angle 3.67139 / 2.56 ( 1660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.80 seconds wall clock time: 103 minutes 27.14 seconds (6207.14 seconds total)