Starting phenix.real_space_refine on Thu Aug 6 06:02:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggc_51327/08_2026/9ggc_51327.map" } resolution = 2.39 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= 0.979 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 41 5.49 5 S 80 5.16 5 C 8747 2.51 5 N 2447 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13930 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7430 Classifications: {'peptide': 933} Link IDs: {'PTRANS': 62, 'TRANS': 870} Chain breaks: 5 Chain: "B" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2850 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 335} Chain breaks: 3 Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2842 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 334} Chain breaks: 3 Chain: "P" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.98, per 1000 atoms: 0.21 Number of scatterers: 13930 At special positions: 0 Unit cell: (103.5, 101.844, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 41 15.00 O 2614 8.00 N 2447 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 679.6 milliseconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3042 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 47.7% alpha, 13.8% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.649A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) 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 203 through 206 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.585A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.854A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.668A pdb=" N GLY A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.591A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 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 430 removed outlier: 4.057A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.635A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.556A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.794A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.545A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.523A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 987 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.992A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.538A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 68 through 76 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 198 removed outlier: 4.671A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.003A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.830A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.809A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.567A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.047A 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 removed outlier: 3.561A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 450 removed outlier: 3.592A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.822A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.956A 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 438 removed outlier: 4.455A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 625 removed outlier: 4.327A pdb=" N PHE A 749 " --> pdb=" O TYR A 739 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.884A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.190A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.979A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.374A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 274 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.541A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.334A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4103 1.34 - 1.45: 2449 1.45 - 1.57: 7606 1.57 - 1.69: 79 1.69 - 1.81: 126 Bond restraints: 14363 Sorted by residual: bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.746 1.610 0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.672 1.606 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C3' DC T 28 " pdb=" C2' DC T 28 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.81e+00 bond pdb=" C3' DG P 20 " pdb=" C2' DG P 20 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.654 1.601 0.053 2.00e-02 2.50e+03 7.04e+00 ... (remaining 14358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 19402 1.96 - 3.93: 216 3.93 - 5.89: 11 5.89 - 7.86: 1 7.86 - 9.82: 1 Bond angle restraints: 19631 Sorted by residual: angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 19626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 7842 17.24 - 34.48: 444 34.48 - 51.72: 138 51.72 - 68.96: 41 68.96 - 86.20: 4 Dihedral angle restraints: 8469 sinusoidal: 3753 harmonic: 4716 Sorted by residual: dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA HIS C 77 " pdb=" C HIS C 77 " pdb=" N PHE C 78 " pdb=" CA PHE C 78 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR C 243 " pdb=" C THR C 243 " pdb=" N PRO C 244 " pdb=" CA PRO C 244 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1693 0.047 - 0.093: 312 0.093 - 0.140: 99 0.140 - 0.187: 0 0.187 - 0.233: 1 Chirality restraints: 2105 Sorted by residual: chirality pdb=" C1' DCP A1302 " pdb=" C2' DCP A1302 " pdb=" N1 DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False 2.25 2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2102 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 73 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1200 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 483 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.019 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 83 2.56 - 3.14: 10415 3.14 - 3.73: 22542 3.73 - 4.31: 31671 4.31 - 4.90: 52236 Nonbonded interactions: 116947 Sorted by model distance: nonbonded pdb="CA CA A1301 " pdb=" O1A DCP A1302 " model vdw 1.974 2.510 nonbonded pdb="CA CA A1301 " pdb=" O2G DCP A1302 " model vdw 2.072 2.510 nonbonded pdb=" OG SER B 80 " pdb=" O GLY B 98 " model vdw 2.206 3.040 nonbonded pdb=" OG SER B 82 " pdb=" OE1 GLN B 85 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 150 " pdb=" O ARG A 288 " model vdw 2.262 3.040 ... (remaining 116942 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 67 through 137 or resid 178 through 218 or resid 230 throu \ gh 482)) selection = (chain 'C' and (resid 67 through 137 or resid 178 through 482)) } 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: 2.160 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.180 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.003 0.136 14363 Z= 0.214 Angle : 0.476 9.819 19631 Z= 0.298 Chirality : 0.040 0.233 2105 Planarity : 0.004 0.041 2388 Dihedral : 12.498 86.197 5427 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.35 % Allowed : 3.03 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1610 helix: 1.65 (0.20), residues: 688 sheet: 0.87 (0.33), residues: 226 loop : 0.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 802 TYR 0.009 0.001 TYR A1108 PHE 0.014 0.001 PHE C 403 TRP 0.010 0.001 TRP A 312 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.21 (14363) covalent geometry : angle 0.47599 / 0.30 (19631) hydrogen bonds : bond 0.15346 / 10.37 ( 672) hydrogen bonds : angle 6.44792 / 4.46 ( 1885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 0.535 Fit side-chains REVERT: A 289 MET cc_start: 0.8447 (ttm) cc_final: 0.8237 (ttm) REVERT: A 361 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7330 (ttm-80) REVERT: A 890 ASP cc_start: 0.7802 (t0) cc_final: 0.7271 (t0) REVERT: B 85 GLN cc_start: 0.7297 (mp10) cc_final: 0.6916 (mp10) REVERT: B 231 ILE cc_start: 0.7264 (mm) cc_final: 0.6980 (mt) REVERT: B 322 LEU cc_start: 0.8290 (mp) cc_final: 0.8011 (mt) REVERT: B 462 MET cc_start: 0.7227 (mmp) cc_final: 0.6953 (mmp) REVERT: B 465 MET cc_start: 0.7614 (mmt) cc_final: 0.7410 (mmt) REVERT: C 180 LYS cc_start: 0.4981 (tppt) cc_final: 0.4637 (tppt) REVERT: C 314 MET cc_start: 0.7432 (mtt) cc_final: 0.7096 (ttm) REVERT: C 422 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5512 (mp10) REVERT: C 449 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5863 (mm-30) outliers start: 5 outliers final: 4 residues processed: 323 average time/residue: 0.6963 time to fit residues: 243.0057 Evaluate side-chains 205 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 201 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 371 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 134 ASN A 390 GLN A 468 ASN A 565 HIS B 187 HIS B 258 HIS B 305 ASN B 309 HIS B 313 HIS B 375 HIS C 258 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.143563 restraints weight = 14020.575| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.12 r_work: 0.3730 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14363 Z= 0.249 Angle : 0.627 6.419 19631 Z= 0.332 Chirality : 0.046 0.169 2105 Planarity : 0.006 0.061 2388 Dihedral : 13.888 59.984 2213 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.31 % Allowed : 11.05 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1610 helix: 1.36 (0.19), residues: 696 sheet: 1.08 (0.33), residues: 221 loop : -0.06 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 807 TYR 0.016 0.002 TYR A 150 PHE 0.021 0.002 PHE A1129 TRP 0.013 0.002 TRP A 441 HIS 0.010 0.002 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (14363) covalent geometry : angle 0.62687 / 0.33 (19631) hydrogen bonds : bond 0.05313 / 3.60 ( 672) hydrogen bonds : angle 5.40464 / 3.65 ( 1885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7574 (mm110) REVERT: A 361 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6669 (ttm-80) REVERT: A 481 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 1121 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: A 1144 GLU cc_start: 0.6677 (mp0) cc_final: 0.6349 (pm20) REVERT: B 71 GLU cc_start: 0.6387 (tp30) cc_final: 0.6103 (tp30) REVERT: B 85 GLN cc_start: 0.6779 (mp10) cc_final: 0.6492 (mp10) REVERT: B 231 ILE cc_start: 0.6111 (mm) cc_final: 0.5645 (mt) REVERT: B 421 MET cc_start: 0.8198 (ptm) cc_final: 0.7766 (tmm) REVERT: C 180 LYS cc_start: 0.3193 (tppt) cc_final: 0.2664 (tppt) REVERT: C 191 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7028 (mt-10) REVERT: C 314 MET cc_start: 0.6933 (mtt) cc_final: 0.6225 (ttm) REVERT: C 386 ASP cc_start: 0.6965 (t0) cc_final: 0.6190 (m-30) REVERT: C 400 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6661 (tm-30) REVERT: C 422 GLN cc_start: 0.6135 (mm-40) cc_final: 0.5476 (mp10) REVERT: C 427 GLN cc_start: 0.6582 (mt0) cc_final: 0.6247 (mp10) REVERT: C 449 GLU cc_start: 0.5272 (mt-10) cc_final: 0.4932 (mm-30) outliers start: 47 outliers final: 19 residues processed: 220 average time/residue: 0.6413 time to fit residues: 153.1059 Evaluate side-chains 199 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.0040 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 258 HIS B 313 HIS B 375 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.180931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134929 restraints weight = 13946.825| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.99 r_work: 0.3699 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14363 Z= 0.166 Angle : 0.541 5.866 19631 Z= 0.288 Chirality : 0.041 0.145 2105 Planarity : 0.005 0.049 2388 Dihedral : 13.918 59.873 2213 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.03 % Allowed : 11.61 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1610 helix: 1.50 (0.19), residues: 690 sheet: 0.94 (0.33), residues: 218 loop : -0.02 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 818 TYR 0.014 0.002 TYR C 432 PHE 0.015 0.002 PHE C 403 TRP 0.019 0.001 TRP B 241 HIS 0.010 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (14363) covalent geometry : angle 0.54138 / 0.29 (19631) hydrogen bonds : bond 0.04362 / 2.97 ( 672) hydrogen bonds : angle 5.11722 / 3.46 ( 1885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.6830 (ttm-80) cc_final: 0.6418 (ttm-80) REVERT: A 385 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5449 (mp) REVERT: A 481 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 1121 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: A 1144 GLU cc_start: 0.6369 (mp0) cc_final: 0.6141 (pm20) REVERT: B 71 GLU cc_start: 0.6224 (tp30) cc_final: 0.5946 (tp30) REVERT: B 85 GLN cc_start: 0.6719 (mp10) cc_final: 0.6392 (mp10) REVERT: B 231 ILE cc_start: 0.5999 (mm) cc_final: 0.5568 (mt) REVERT: B 322 LEU cc_start: 0.6566 (mp) cc_final: 0.6325 (mt) REVERT: B 421 MET cc_start: 0.8039 (ptm) cc_final: 0.7064 (pp-130) REVERT: C 180 LYS cc_start: 0.2817 (tppt) cc_final: 0.2363 (tppt) REVERT: C 191 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6889 (mt-10) REVERT: C 314 MET cc_start: 0.6740 (mtt) cc_final: 0.6039 (ttm) REVERT: C 386 ASP cc_start: 0.7039 (t0) cc_final: 0.6669 (t0) REVERT: C 400 GLN cc_start: 0.6611 (mm-40) cc_final: 0.6290 (tm-30) REVERT: C 422 GLN cc_start: 0.6160 (mm-40) cc_final: 0.5568 (mp10) REVERT: C 427 GLN cc_start: 0.6572 (mt0) cc_final: 0.6090 (mp10) REVERT: C 449 GLU cc_start: 0.4996 (mt-10) cc_final: 0.4604 (mm-30) outliers start: 43 outliers final: 19 residues processed: 219 average time/residue: 0.6670 time to fit residues: 159.0453 Evaluate side-chains 199 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 258 HIS B 313 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134369 restraints weight = 13989.252| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.99 r_work: 0.3692 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14363 Z= 0.162 Angle : 0.537 6.313 19631 Z= 0.286 Chirality : 0.041 0.146 2105 Planarity : 0.005 0.047 2388 Dihedral : 13.928 59.730 2213 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.74 % Allowed : 13.37 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1610 helix: 1.58 (0.19), residues: 690 sheet: 0.93 (0.33), residues: 220 loop : 0.00 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 818 TYR 0.015 0.002 TYR B 291 PHE 0.015 0.002 PHE C 403 TRP 0.021 0.001 TRP B 241 HIS 0.013 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14363) covalent geometry : angle 0.53696 / 0.29 (19631) hydrogen bonds : bond 0.04201 / 2.87 ( 672) hydrogen bonds : angle 5.03641 / 3.40 ( 1885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.6795 (ttm-80) cc_final: 0.6380 (ttm-80) REVERT: A 385 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.5458 (mp) REVERT: A 481 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 1121 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6385 (tm-30) REVERT: B 85 GLN cc_start: 0.6840 (mp10) cc_final: 0.6539 (mp10) REVERT: B 231 ILE cc_start: 0.6022 (mm) cc_final: 0.5587 (mt) REVERT: B 322 LEU cc_start: 0.6624 (mp) cc_final: 0.6384 (mt) REVERT: B 450 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.6331 (p0) REVERT: C 180 LYS cc_start: 0.2841 (tppt) cc_final: 0.2378 (tppt) REVERT: C 258 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5696 (m170) REVERT: C 314 MET cc_start: 0.6722 (mtt) cc_final: 0.6021 (ttm) REVERT: C 386 ASP cc_start: 0.7057 (t0) cc_final: 0.6670 (t0) REVERT: C 400 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6291 (tm-30) REVERT: C 422 GLN cc_start: 0.6237 (mm-40) cc_final: 0.5645 (mp10) REVERT: C 427 GLN cc_start: 0.6527 (mt0) cc_final: 0.6071 (mp10) REVERT: C 449 GLU cc_start: 0.4977 (mt-10) cc_final: 0.4599 (mm-30) REVERT: C 466 MET cc_start: 0.7967 (ttm) cc_final: 0.7581 (ttm) outliers start: 39 outliers final: 21 residues processed: 214 average time/residue: 0.6344 time to fit residues: 148.0064 Evaluate side-chains 202 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 128 optimal weight: 0.0170 chunk 165 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 258 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.178101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139928 restraints weight = 14015.786| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.19 r_work: 0.3628 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14363 Z= 0.218 Angle : 0.599 7.278 19631 Z= 0.315 Chirality : 0.044 0.149 2105 Planarity : 0.005 0.050 2388 Dihedral : 14.024 59.914 2213 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.38 % Allowed : 12.95 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.89 (0.20), residues: 1610 helix: 1.31 (0.19), residues: 693 sheet: 0.66 (0.33), residues: 224 loop : -0.07 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 807 TYR 0.016 0.002 TYR A 150 PHE 0.015 0.002 PHE A1129 TRP 0.021 0.002 TRP B 241 HIS 0.015 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (14363) covalent geometry : angle 0.59942 / 0.32 (19631) hydrogen bonds : bond 0.04659 / 3.18 ( 672) hydrogen bonds : angle 5.15083 / 3.49 ( 1885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5972 (mp) REVERT: A 361 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6566 (ttm-80) REVERT: A 371 LYS cc_start: 0.8412 (ptmt) cc_final: 0.7772 (ptpp) REVERT: A 385 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5536 (mp) REVERT: A 581 ASP cc_start: 0.6974 (m-30) cc_final: 0.6701 (p0) REVERT: A 598 VAL cc_start: 0.6590 (m) cc_final: 0.6354 (p) REVERT: A 833 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8049 (tp30) REVERT: A 1121 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: B 85 GLN cc_start: 0.6716 (mp10) cc_final: 0.6442 (mp10) REVERT: B 231 ILE cc_start: 0.6092 (mm) cc_final: 0.5645 (mt) REVERT: B 322 LEU cc_start: 0.6530 (mp) cc_final: 0.6301 (mt) REVERT: B 394 GLU cc_start: 0.7606 (tp30) cc_final: 0.7329 (tp30) REVERT: B 450 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6292 (p0) REVERT: C 180 LYS cc_start: 0.2913 (tppt) cc_final: 0.2644 (tppt) REVERT: C 258 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.5734 (m170) REVERT: C 314 MET cc_start: 0.6668 (mtt) cc_final: 0.5958 (ttm) REVERT: C 386 ASP cc_start: 0.7134 (t0) cc_final: 0.6716 (t0) REVERT: C 400 GLN cc_start: 0.6746 (mm-40) cc_final: 0.6380 (tm-30) REVERT: C 422 GLN cc_start: 0.6184 (mm-40) cc_final: 0.5226 (mt0) REVERT: C 427 GLN cc_start: 0.6520 (mt0) cc_final: 0.6078 (mp10) REVERT: C 449 GLU cc_start: 0.4970 (mt-10) cc_final: 0.4596 (mm-30) outliers start: 48 outliers final: 26 residues processed: 218 average time/residue: 0.6198 time to fit residues: 147.7207 Evaluate side-chains 206 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 959 GLN A1110 HIS B 258 HIS B 287 ASN B 313 HIS C 96 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.179034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.141010 restraints weight = 14077.196| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.11 r_work: 0.3704 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14363 Z= 0.211 Angle : 0.592 7.471 19631 Z= 0.312 Chirality : 0.043 0.148 2105 Planarity : 0.005 0.049 2388 Dihedral : 14.042 59.952 2213 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.89 % Allowed : 13.93 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1610 helix: 1.28 (0.19), residues: 693 sheet: 0.57 (0.32), residues: 224 loop : -0.08 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 818 TYR 0.020 0.002 TYR A 479 PHE 0.015 0.002 PHE A1129 TRP 0.023 0.002 TRP B 241 HIS 0.015 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (14363) covalent geometry : angle 0.59199 / 0.31 (19631) hydrogen bonds : bond 0.04526 / 3.09 ( 672) hydrogen bonds : angle 5.14706 / 3.49 ( 1885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6175 (mp) REVERT: A 361 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6757 (ttm-80) REVERT: A 371 LYS cc_start: 0.8478 (ptmt) cc_final: 0.7731 (ptpp) REVERT: A 385 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.5703 (mp) REVERT: A 481 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 581 ASP cc_start: 0.7050 (m-30) cc_final: 0.6794 (p0) REVERT: A 598 VAL cc_start: 0.6730 (m) cc_final: 0.6526 (p) REVERT: A 833 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8096 (tp30) REVERT: B 71 GLU cc_start: 0.6473 (tp30) cc_final: 0.6191 (tp30) REVERT: B 85 GLN cc_start: 0.6970 (mp10) cc_final: 0.6716 (mp10) REVERT: B 185 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5468 (mt) REVERT: B 231 ILE cc_start: 0.6300 (mm) cc_final: 0.5834 (mt) REVERT: B 450 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6555 (p0) REVERT: C 180 LYS cc_start: 0.3092 (tppt) cc_final: 0.2786 (tppt) REVERT: C 258 HIS cc_start: 0.6172 (OUTLIER) cc_final: 0.5853 (m170) REVERT: C 314 MET cc_start: 0.6781 (mtt) cc_final: 0.6085 (ttm) REVERT: C 449 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4814 (mm-30) REVERT: C 466 MET cc_start: 0.8123 (ttm) cc_final: 0.7758 (ttm) REVERT: C 469 SER cc_start: 0.8230 (t) cc_final: 0.7719 (p) outliers start: 41 outliers final: 26 residues processed: 209 average time/residue: 0.5407 time to fit residues: 123.9419 Evaluate side-chains 215 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 HIS B 258 HIS B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.180167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.142340 restraints weight = 14030.474| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.10 r_work: 0.3720 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14363 Z= 0.169 Angle : 0.560 7.674 19631 Z= 0.296 Chirality : 0.041 0.146 2105 Planarity : 0.005 0.049 2388 Dihedral : 14.021 59.937 2213 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.38 % Allowed : 13.65 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.94 (0.20), residues: 1610 helix: 1.37 (0.19), residues: 693 sheet: 0.59 (0.32), residues: 224 loop : -0.03 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.021 0.002 TYR A 479 PHE 0.014 0.001 PHE C 403 TRP 0.026 0.002 TRP B 241 HIS 0.014 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (14363) covalent geometry : angle 0.55993 / 0.30 (19631) hydrogen bonds : bond 0.04249 / 2.90 ( 672) hydrogen bonds : angle 5.07746 / 3.44 ( 1885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6152 (mp) REVERT: A 361 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6700 (ttm-80) REVERT: A 371 LYS cc_start: 0.8449 (ptmt) cc_final: 0.7703 (ptpp) REVERT: A 385 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.5626 (mp) REVERT: A 581 ASP cc_start: 0.6999 (m-30) cc_final: 0.6753 (p0) REVERT: A 833 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8133 (tp30) REVERT: A 1121 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6577 (tm-30) REVERT: B 71 GLU cc_start: 0.6456 (tp30) cc_final: 0.6159 (tp30) REVERT: B 85 GLN cc_start: 0.6943 (mp10) cc_final: 0.6613 (mp10) REVERT: B 231 ILE cc_start: 0.6269 (mm) cc_final: 0.5793 (mt) REVERT: B 322 LEU cc_start: 0.6748 (mp) cc_final: 0.6509 (mt) REVERT: B 450 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6622 (p0) REVERT: B 468 ILE cc_start: 0.6610 (mm) cc_final: 0.6324 (tp) REVERT: C 71 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: C 180 LYS cc_start: 0.3093 (tppt) cc_final: 0.2796 (tppt) REVERT: C 258 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5839 (m170) REVERT: C 314 MET cc_start: 0.6743 (mtt) cc_final: 0.6043 (ttm) REVERT: C 400 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6591 (tm-30) REVERT: C 422 GLN cc_start: 0.6211 (mm-40) cc_final: 0.5225 (mt0) REVERT: C 427 GLN cc_start: 0.6657 (mt0) cc_final: 0.6189 (mp10) REVERT: C 449 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4802 (mm-30) REVERT: C 466 MET cc_start: 0.8172 (ttm) cc_final: 0.7752 (ttm) REVERT: C 469 SER cc_start: 0.8234 (t) cc_final: 0.7725 (p) outliers start: 48 outliers final: 28 residues processed: 217 average time/residue: 0.5621 time to fit residues: 133.4596 Evaluate side-chains 216 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 146 optimal weight: 10.0000 chunk 121 optimal weight: 0.2980 chunk 148 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 HIS B 258 HIS B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140917 restraints weight = 13972.078| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.07 r_work: 0.3705 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14363 Z= 0.222 Angle : 0.606 7.977 19631 Z= 0.318 Chirality : 0.044 0.148 2105 Planarity : 0.005 0.049 2388 Dihedral : 14.052 59.678 2213 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.45 % Allowed : 13.72 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.79 (0.20), residues: 1610 helix: 1.23 (0.19), residues: 693 sheet: 0.54 (0.32), residues: 224 loop : -0.10 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 818 TYR 0.024 0.002 TYR A 479 PHE 0.016 0.002 PHE A1129 TRP 0.028 0.002 TRP B 241 HIS 0.016 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (14363) covalent geometry : angle 0.60556 / 0.32 (19631) hydrogen bonds : bond 0.04567 / 3.11 ( 672) hydrogen bonds : angle 5.14627 / 3.49 ( 1885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6146 (mp) REVERT: A 361 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6734 (ttm-80) REVERT: A 371 LYS cc_start: 0.8452 (ptmt) cc_final: 0.7719 (ptpp) REVERT: A 385 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.5699 (mp) REVERT: A 481 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: A 581 ASP cc_start: 0.7058 (m-30) cc_final: 0.6770 (p0) REVERT: A 833 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8045 (tp30) REVERT: A 1121 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: B 85 GLN cc_start: 0.6927 (mp10) cc_final: 0.6624 (mp10) REVERT: B 122 ARG cc_start: 0.7098 (tpp-160) cc_final: 0.6589 (mpt180) REVERT: B 185 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5502 (mt) REVERT: B 231 ILE cc_start: 0.6295 (mm) cc_final: 0.5823 (mt) REVERT: B 322 LEU cc_start: 0.6787 (mp) cc_final: 0.6550 (mt) REVERT: B 394 GLU cc_start: 0.7567 (tp30) cc_final: 0.7310 (tp30) REVERT: B 397 GLN cc_start: 0.7401 (mp-120) cc_final: 0.7181 (mp-120) REVERT: B 450 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6674 (p0) REVERT: B 468 ILE cc_start: 0.6624 (mm) cc_final: 0.6344 (tp) REVERT: C 71 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6141 (tt0) REVERT: C 180 LYS cc_start: 0.3063 (tppt) cc_final: 0.2770 (tppt) REVERT: C 258 HIS cc_start: 0.6215 (OUTLIER) cc_final: 0.5905 (m170) REVERT: C 400 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6636 (tm-30) REVERT: C 422 GLN cc_start: 0.6205 (mm-40) cc_final: 0.5187 (mt0) REVERT: C 427 GLN cc_start: 0.6653 (mt0) cc_final: 0.6184 (mp10) REVERT: C 449 GLU cc_start: 0.5240 (mt-10) cc_final: 0.4848 (mm-30) REVERT: C 466 MET cc_start: 0.8173 (ttm) cc_final: 0.7727 (ttm) REVERT: C 469 SER cc_start: 0.8231 (t) cc_final: 0.7719 (p) outliers start: 49 outliers final: 31 residues processed: 215 average time/residue: 0.6076 time to fit residues: 142.8624 Evaluate side-chains 217 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 HIS B 258 HIS B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135667 restraints weight = 14144.728| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.97 r_work: 0.3750 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14363 Z= 0.138 Angle : 0.531 7.698 19631 Z= 0.282 Chirality : 0.040 0.142 2105 Planarity : 0.004 0.048 2388 Dihedral : 13.994 59.891 2213 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.53 % Allowed : 14.64 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1610 helix: 1.50 (0.19), residues: 693 sheet: 0.69 (0.32), residues: 232 loop : 0.05 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.022 0.002 TYR A 479 PHE 0.015 0.001 PHE C 403 TRP 0.034 0.001 TRP B 241 HIS 0.015 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14363) covalent geometry : angle 0.53109 / 0.28 (19631) hydrogen bonds : bond 0.03925 / 2.68 ( 672) hydrogen bonds : angle 4.97527 / 3.38 ( 1885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6004 (ttt90) cc_final: 0.5701 (ttt90) REVERT: A 226 GLN cc_start: 0.7246 (mt0) cc_final: 0.6680 (pt0) REVERT: A 361 ARG cc_start: 0.6935 (ttm-80) cc_final: 0.6566 (ttm-80) REVERT: A 371 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7657 (ptpp) REVERT: A 385 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5513 (mp) REVERT: A 581 ASP cc_start: 0.6964 (m-30) cc_final: 0.6730 (p0) REVERT: A 833 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8015 (tp30) REVERT: B 85 GLN cc_start: 0.6853 (mp10) cc_final: 0.6540 (mp10) REVERT: B 122 ARG cc_start: 0.6973 (tpp-160) cc_final: 0.6425 (mpt180) REVERT: B 231 ILE cc_start: 0.6199 (mm) cc_final: 0.5727 (mt) REVERT: B 322 LEU cc_start: 0.6691 (mp) cc_final: 0.6462 (mt) REVERT: B 450 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6603 (p0) REVERT: C 180 LYS cc_start: 0.2901 (tppt) cc_final: 0.2624 (tppt) REVERT: C 258 HIS cc_start: 0.6106 (OUTLIER) cc_final: 0.5702 (m170) REVERT: C 400 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6477 (tm-30) REVERT: C 422 GLN cc_start: 0.6240 (mm-40) cc_final: 0.5595 (mp10) REVERT: C 427 GLN cc_start: 0.6627 (mt0) cc_final: 0.6145 (mp10) REVERT: C 449 GLU cc_start: 0.5070 (mt-10) cc_final: 0.4694 (mm-30) REVERT: C 466 MET cc_start: 0.8058 (ttm) cc_final: 0.7570 (ttm) REVERT: C 469 SER cc_start: 0.8199 (t) cc_final: 0.7708 (p) outliers start: 36 outliers final: 25 residues processed: 209 average time/residue: 0.6141 time to fit residues: 140.3683 Evaluate side-chains 208 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 0.0670 chunk 114 optimal weight: 0.0030 chunk 142 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 HIS B 258 HIS B 313 HIS B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.179933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142149 restraints weight = 14035.186| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.04 r_work: 0.3726 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14363 Z= 0.186 Angle : 0.572 8.029 19631 Z= 0.302 Chirality : 0.042 0.146 2105 Planarity : 0.005 0.049 2388 Dihedral : 14.002 59.794 2212 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.53 % Allowed : 14.99 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.99 (0.20), residues: 1610 helix: 1.39 (0.19), residues: 693 sheet: 0.68 (0.32), residues: 232 loop : -0.00 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.026 0.002 TYR A 479 PHE 0.014 0.002 PHE A1129 TRP 0.034 0.002 TRP B 241 HIS 0.016 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (14363) covalent geometry : angle 0.57181 / 0.30 (19631) hydrogen bonds : bond 0.04253 / 2.90 ( 672) hydrogen bonds : angle 5.02363 / 3.41 ( 1885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6112 (ttt90) cc_final: 0.5843 (ttt90) REVERT: A 226 GLN cc_start: 0.7336 (mt0) cc_final: 0.6780 (pt0) REVERT: A 361 ARG cc_start: 0.7079 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: A 371 LYS cc_start: 0.8433 (ptmt) cc_final: 0.7704 (ptpp) REVERT: A 385 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.5641 (mp) REVERT: A 481 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 581 ASP cc_start: 0.7036 (m-30) cc_final: 0.6778 (p0) REVERT: A 830 ASP cc_start: 0.7351 (m-30) cc_final: 0.6478 (t0) REVERT: A 833 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8044 (tp30) REVERT: B 85 GLN cc_start: 0.6950 (mp10) cc_final: 0.6637 (mp10) REVERT: B 122 ARG cc_start: 0.7077 (tpp-160) cc_final: 0.6476 (mpt180) REVERT: B 185 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5509 (mt) REVERT: B 231 ILE cc_start: 0.6304 (mm) cc_final: 0.5826 (mt) REVERT: B 394 GLU cc_start: 0.7579 (tp30) cc_final: 0.7026 (mp0) REVERT: B 450 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6740 (p0) REVERT: C 180 LYS cc_start: 0.3064 (tppt) cc_final: 0.2815 (tppt) REVERT: C 258 HIS cc_start: 0.6161 (OUTLIER) cc_final: 0.5840 (m170) REVERT: C 400 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6642 (tm-30) REVERT: C 422 GLN cc_start: 0.6252 (mm-40) cc_final: 0.5592 (mp10) REVERT: C 427 GLN cc_start: 0.6688 (mt0) cc_final: 0.6194 (mp10) REVERT: C 449 GLU cc_start: 0.5247 (mt-10) cc_final: 0.4869 (mm-30) REVERT: C 466 MET cc_start: 0.8170 (ttm) cc_final: 0.7679 (ttm) REVERT: C 469 SER cc_start: 0.8253 (t) cc_final: 0.7769 (p) outliers start: 36 outliers final: 26 residues processed: 204 average time/residue: 0.6198 time to fit residues: 138.3222 Evaluate side-chains 209 residues out of total 1421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 50 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1110 HIS B 258 HIS B 313 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.179536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.141861 restraints weight = 14001.253| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.07 r_work: 0.3722 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14363 Z= 0.190 Angle : 0.580 8.009 19631 Z= 0.306 Chirality : 0.042 0.146 2105 Planarity : 0.005 0.049 2388 Dihedral : 14.014 59.969 2212 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.67 % Allowed : 14.85 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % 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: 0.96 (0.20), residues: 1610 helix: 1.36 (0.19), residues: 693 sheet: 0.67 (0.32), residues: 232 loop : -0.01 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 818 TYR 0.025 0.002 TYR A 479 PHE 0.013 0.002 PHE A1129 TRP 0.036 0.002 TRP B 241 HIS 0.016 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (14363) covalent geometry : angle 0.57980 / 0.31 (19631) hydrogen bonds : bond 0.04303 / 2.93 ( 672) hydrogen bonds : angle 5.04236 / 3.42 ( 1885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6254.66 seconds wall clock time: 106 minutes 57.32 seconds (6417.32 seconds total)