Starting phenix.real_space_refine on Thu Aug 6 06:10:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggf_51330/08_2026/9ggf_51330.map" } resolution = 2.65 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= 0.002 sd= 0.975 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 8745 2.51 5 N 2446 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13925 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7425 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 62, 'TRANS': 869} 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: 2.65, per 1000 atoms: 0.19 Number of scatterers: 13925 At special positions: 0 Unit cell: (94.875, 104.775, 144.375, 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 2612 8.00 N 2446 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 470.9 milliseconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3038 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 47.0% alpha, 14.4% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 removed outlier: 4.223A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.570A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 6.651A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.583A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 432 removed outlier: 3.928A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.633A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.611A pdb=" N LEU A 558 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.840A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 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 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.751A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 874 through 878 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 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 986 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.719A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.724A 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 120 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.070A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 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: 3.657A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (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: 4.091A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.598A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.806A 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: 4.154A 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 353 Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.699A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.814A 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 187 removed outlier: 3.689A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.193A 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: 4.823A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 7.550A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.596A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.052A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 307 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER C 337 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN C 305 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN C 339 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 303 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP C 341 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU C 301 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB2, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.122A pdb=" N LYS C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.192A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3966 1.33 - 1.45: 2578 1.45 - 1.57: 7610 1.57 - 1.69: 79 1.69 - 1.81: 126 Bond restraints: 14359 Sorted by residual: bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.746 1.612 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C3' DG P 20 " pdb=" C2' DG P 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C3' DC P 15 " pdb=" C2' DC P 15 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C3' DC T 28 " pdb=" C2' DC T 28 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.99e+00 ... (remaining 14354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 19343 1.80 - 3.61: 259 3.61 - 5.41: 20 5.41 - 7.21: 2 7.21 - 9.02: 1 Bond angle restraints: 19625 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 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O4 DT T 22 " pdb=" C4 DT T 22 " pdb=" C5 DT T 22 " ideal model delta sigma weight residual 124.90 121.96 2.94 7.00e-01 2.04e+00 1.77e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 19620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7922 17.97 - 35.95: 381 35.95 - 53.92: 135 53.92 - 71.89: 22 71.89 - 89.87: 3 Dihedral angle restraints: 8463 sinusoidal: 3751 harmonic: 4712 Sorted by residual: dihedral pdb=" CA VAL A 196 " pdb=" C VAL A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual -180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 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 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" N GLN A 564 " pdb=" CA GLN A 564 " pdb=" CB GLN A 564 " pdb=" CG GLN A 564 " ideal model delta sinusoidal sigma weight residual -60.00 -117.44 57.44 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 8460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1689 0.046 - 0.093: 305 0.093 - 0.139: 106 0.139 - 0.185: 0 0.185 - 0.232: 1 Chirality restraints: 2101 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 1.34e+00 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 840 " pdb=" N ILE A 840 " pdb=" C ILE A 840 " pdb=" CB ILE A 840 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 2098 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+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 GLY A 782 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 783 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 783 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 783 " 0.022 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 3.79e-02 2.30e+00 pdb=" N PRO A1200 " 0.066 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 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 15 2.36 - 2.99: 6755 2.99 - 3.63: 20606 3.63 - 4.26: 33058 4.26 - 4.90: 54631 Nonbonded interactions: 115065 Sorted by model distance: nonbonded pdb=" OD2 ASP A1135 " pdb="CA CA A1301 " model vdw 1.725 2.510 nonbonded pdb="CA CA A1301 " pdb=" O1B DCP A1302 " model vdw 1.815 2.510 nonbonded pdb=" OG SER A 272 " pdb=" O VAL A 844 " model vdw 2.202 3.040 nonbonded pdb="CA CA A1301 " pdb=" O2G DCP A1302 " model vdw 2.250 2.510 nonbonded pdb=" O SER C 117 " pdb=" NH1 ARG C 122 " model vdw 2.291 3.120 ... (remaining 115060 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 0.134 14359 Z= 0.219 Angle : 0.492 9.015 19625 Z= 0.313 Chirality : 0.040 0.232 2101 Planarity : 0.004 0.042 2388 Dihedral : 12.125 89.866 5425 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.56 % Allowed : 2.54 % Favored : 96.90 % 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: 1.34 (0.21), residues: 1609 helix: 1.64 (0.20), residues: 700 sheet: 0.92 (0.33), residues: 236 loop : 0.18 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 456 TYR 0.010 0.001 TYR A 150 PHE 0.015 0.001 PHE C 403 TRP 0.009 0.001 TRP A 312 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.22 (14359) covalent geometry : angle 0.49173 / 0.31 (19625) hydrogen bonds : bond 0.15731 / 10.75 ( 675) hydrogen bonds : angle 6.44540 / 4.78 ( 1894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 316 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6378 (ttt-90) cc_final: 0.5669 (ttp80) REVERT: A 193 ARG cc_start: 0.7401 (mtm180) cc_final: 0.6177 (mmp80) REVERT: A 232 ARG cc_start: 0.6691 (mtt180) cc_final: 0.6128 (mtm180) REVERT: A 459 MET cc_start: 0.8211 (tpp) cc_final: 0.7788 (tmm) REVERT: A 773 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7544 (mppt) REVERT: A 856 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 1089 GLN cc_start: 0.7272 (mt0) cc_final: 0.7028 (mp10) REVERT: B 134 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7507 (mmtt) REVERT: B 250 GLN cc_start: 0.7203 (mt0) cc_final: 0.6943 (mm-40) REVERT: B 461 THR cc_start: 0.6800 (p) cc_final: 0.6576 (p) REVERT: C 407 LEU cc_start: 0.7983 (mt) cc_final: 0.7780 (mm) REVERT: C 411 ILE cc_start: 0.8431 (mt) cc_final: 0.8214 (mt) outliers start: 8 outliers final: 3 residues processed: 323 average time/residue: 0.5598 time to fit residues: 196.8384 Evaluate side-chains 193 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain C residue 128 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: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN A1134 HIS B 258 HIS B 272 ASN B 287 ASN B 330 ASN B 397 GLN C 184 ASN C 187 HIS C 287 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125446 restraints weight = 14832.489| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.12 r_work: 0.3556 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14359 Z= 0.239 Angle : 0.645 10.371 19625 Z= 0.338 Chirality : 0.045 0.197 2101 Planarity : 0.006 0.050 2388 Dihedral : 14.099 108.113 2213 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.17 % Allowed : 11.28 % Favored : 85.55 % 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: 1.04 (0.20), residues: 1609 helix: 1.28 (0.19), residues: 704 sheet: 0.99 (0.32), residues: 237 loop : 0.06 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1071 TYR 0.018 0.003 TYR B 291 PHE 0.020 0.002 PHE A1129 TRP 0.015 0.002 TRP B 241 HIS 0.007 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (14359) covalent geometry : angle 0.64542 / 0.34 (19625) hydrogen bonds : bond 0.04999 / 3.41 ( 675) hydrogen bonds : angle 5.26546 / 3.91 ( 1894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6736 (mm) REVERT: A 177 ARG cc_start: 0.6112 (ttt-90) cc_final: 0.5133 (ttp80) REVERT: A 193 ARG cc_start: 0.7279 (mtm180) cc_final: 0.5301 (mmp80) REVERT: A 232 ARG cc_start: 0.6421 (mtt180) cc_final: 0.5568 (mtm180) REVERT: A 263 GLU cc_start: 0.7428 (mp0) cc_final: 0.6886 (mp0) REVERT: A 459 MET cc_start: 0.8558 (tpp) cc_final: 0.7904 (tmm) REVERT: A 773 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6688 (mppt) REVERT: A 1089 GLN cc_start: 0.7156 (mt0) cc_final: 0.6695 (mp10) REVERT: B 134 LYS cc_start: 0.7388 (ttpt) cc_final: 0.6293 (mmtt) REVERT: B 250 GLN cc_start: 0.7386 (mt0) cc_final: 0.6649 (mm-40) REVERT: B 325 ARG cc_start: 0.6177 (mtt90) cc_final: 0.5831 (mtm110) REVERT: C 236 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7311 (mm-30) REVERT: C 249 ASN cc_start: 0.5838 (m-40) cc_final: 0.5567 (m110) REVERT: C 334 CYS cc_start: 0.6940 (m) cc_final: 0.6073 (t) REVERT: C 370 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8080 (mttt) outliers start: 45 outliers final: 16 residues processed: 213 average time/residue: 0.5778 time to fit residues: 134.0270 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 397 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.164192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125532 restraints weight = 14880.201| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.15 r_work: 0.3569 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14359 Z= 0.164 Angle : 0.563 10.595 19625 Z= 0.294 Chirality : 0.042 0.170 2101 Planarity : 0.005 0.050 2388 Dihedral : 13.975 89.680 2212 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.47 % Allowed : 12.97 % Favored : 84.57 % 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: 1.09 (0.20), residues: 1609 helix: 1.35 (0.20), residues: 704 sheet: 1.00 (0.32), residues: 237 loop : 0.06 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1071 TYR 0.020 0.002 TYR A1166 PHE 0.025 0.002 PHE A 88 TRP 0.017 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14359) covalent geometry : angle 0.56323 / 0.29 (19625) hydrogen bonds : bond 0.04097 / 2.81 ( 675) hydrogen bonds : angle 4.97720 / 3.72 ( 1894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 177 ARG cc_start: 0.6085 (ttt-90) cc_final: 0.5011 (ttp80) REVERT: A 193 ARG cc_start: 0.7158 (mtm180) cc_final: 0.5153 (mmp80) REVERT: A 232 ARG cc_start: 0.6269 (mtt180) cc_final: 0.5447 (mtm180) REVERT: A 263 GLU cc_start: 0.7392 (mp0) cc_final: 0.7115 (mp0) REVERT: A 459 MET cc_start: 0.8527 (tpp) cc_final: 0.7878 (tmm) REVERT: A 494 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7468 (pm20) REVERT: A 773 LYS cc_start: 0.7414 (mmmt) cc_final: 0.6566 (mppt) REVERT: A 776 ASP cc_start: 0.7986 (t0) cc_final: 0.7694 (t0) REVERT: A 1089 GLN cc_start: 0.7043 (mt0) cc_final: 0.6589 (mp10) REVERT: B 134 LYS cc_start: 0.7382 (ttpt) cc_final: 0.6163 (mmtt) REVERT: B 250 GLN cc_start: 0.7397 (mt0) cc_final: 0.6656 (mm-40) REVERT: B 308 ASP cc_start: 0.7476 (p0) cc_final: 0.7173 (p0) REVERT: B 325 ARG cc_start: 0.6179 (mtt90) cc_final: 0.5894 (mtm110) REVERT: C 236 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: C 249 ASN cc_start: 0.5751 (m-40) cc_final: 0.5523 (m110) REVERT: C 325 ARG cc_start: 0.5572 (mtm110) cc_final: 0.4840 (mmm160) REVERT: C 334 CYS cc_start: 0.6909 (m) cc_final: 0.5985 (t) REVERT: C 370 LYS cc_start: 0.8327 (mmtm) cc_final: 0.8069 (mttt) outliers start: 35 outliers final: 17 residues processed: 195 average time/residue: 0.5973 time to fit residues: 126.8260 Evaluate side-chains 187 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 397 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 6 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 0.1980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.0070 chunk 154 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN A 922 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.165520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126672 restraints weight = 14879.909| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.16 r_work: 0.3585 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14359 Z= 0.123 Angle : 0.525 10.119 19625 Z= 0.275 Chirality : 0.040 0.155 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.911 89.492 2210 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.54 % Allowed : 13.25 % Favored : 84.21 % 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: 1.30 (0.21), residues: 1609 helix: 1.57 (0.20), residues: 704 sheet: 1.05 (0.32), residues: 237 loop : 0.13 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.020 0.002 PHE A 88 TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14359) covalent geometry : angle 0.52544 / 0.28 (19625) hydrogen bonds : bond 0.03594 / 2.47 ( 675) hydrogen bonds : angle 4.78892 / 3.58 ( 1894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.484 Fit side-chains REVERT: A 177 ARG cc_start: 0.5974 (ttt-90) cc_final: 0.4915 (ttp80) REVERT: A 192 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6414 (mm-30) REVERT: A 193 ARG cc_start: 0.7085 (mtm180) cc_final: 0.5082 (mmp80) REVERT: A 232 ARG cc_start: 0.6154 (mtt180) cc_final: 0.5478 (mtm180) REVERT: A 263 GLU cc_start: 0.7408 (mp0) cc_final: 0.7124 (mp0) REVERT: A 459 MET cc_start: 0.8527 (tpp) cc_final: 0.7874 (tmm) REVERT: A 494 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7374 (pm20) REVERT: A 559 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5024 (mt) REVERT: A 773 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6375 (mppt) REVERT: A 776 ASP cc_start: 0.7946 (t0) cc_final: 0.7644 (t0) REVERT: A 922 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5746 (mt0) REVERT: A 1089 GLN cc_start: 0.6971 (mt0) cc_final: 0.6561 (mp10) REVERT: B 134 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6045 (mmtt) REVERT: B 250 GLN cc_start: 0.7226 (mt0) cc_final: 0.6423 (mm-40) REVERT: B 308 ASP cc_start: 0.7463 (p0) cc_final: 0.7127 (p0) REVERT: B 325 ARG cc_start: 0.6154 (mtt90) cc_final: 0.5909 (mtm110) REVERT: C 183 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: C 236 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: C 249 ASN cc_start: 0.5697 (m-40) cc_final: 0.5478 (m110) REVERT: C 325 ARG cc_start: 0.5554 (mtm110) cc_final: 0.4789 (mmm160) REVERT: C 334 CYS cc_start: 0.6758 (m) cc_final: 0.5868 (t) REVERT: C 370 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8035 (mttt) REVERT: C 419 GLU cc_start: 0.8069 (tp30) cc_final: 0.7587 (tp30) REVERT: C 421 MET cc_start: 0.7897 (ppp) cc_final: 0.7428 (ppp) outliers start: 36 outliers final: 15 residues processed: 197 average time/residue: 0.5602 time to fit residues: 120.6384 Evaluate side-chains 185 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 736 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125550 restraints weight = 14809.420| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.15 r_work: 0.3572 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14359 Z= 0.147 Angle : 0.547 10.435 19625 Z= 0.283 Chirality : 0.041 0.173 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.921 88.640 2210 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.26 % Allowed : 13.95 % Favored : 83.79 % 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: 1.28 (0.21), residues: 1609 helix: 1.56 (0.20), residues: 704 sheet: 1.08 (0.32), residues: 231 loop : 0.11 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1071 TYR 0.020 0.002 TYR A1166 PHE 0.020 0.002 PHE A 88 TRP 0.018 0.001 TRP B 241 HIS 0.006 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14359) covalent geometry : angle 0.54695 / 0.28 (19625) hydrogen bonds : bond 0.03708 / 2.56 ( 675) hydrogen bonds : angle 4.77083 / 3.58 ( 1894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.417 Fit side-chains REVERT: A 177 ARG cc_start: 0.6007 (ttt-90) cc_final: 0.4946 (ttp80) REVERT: A 193 ARG cc_start: 0.7102 (mtm180) cc_final: 0.5153 (mmp80) REVERT: A 263 GLU cc_start: 0.7432 (mp0) cc_final: 0.7113 (mp0) REVERT: A 391 ASP cc_start: 0.7121 (m-30) cc_final: 0.6909 (m-30) REVERT: A 459 MET cc_start: 0.8540 (tpp) cc_final: 0.7890 (tmm) REVERT: A 494 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7390 (pm20) REVERT: A 559 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.4981 (mt) REVERT: A 776 ASP cc_start: 0.7963 (t0) cc_final: 0.7681 (t0) REVERT: A 1089 GLN cc_start: 0.6982 (mt0) cc_final: 0.6583 (mp10) REVERT: B 124 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6452 (pm20) REVERT: B 134 LYS cc_start: 0.7279 (ttpt) cc_final: 0.5977 (mmtt) REVERT: B 250 GLN cc_start: 0.7238 (mt0) cc_final: 0.6479 (mm-40) REVERT: B 308 ASP cc_start: 0.7452 (p0) cc_final: 0.7094 (p0) REVERT: B 325 ARG cc_start: 0.6207 (mtt90) cc_final: 0.5936 (mtm110) REVERT: B 450 ASN cc_start: 0.6507 (p0) cc_final: 0.6224 (p0) REVERT: C 236 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: C 249 ASN cc_start: 0.5700 (m-40) cc_final: 0.5469 (m110) REVERT: C 325 ARG cc_start: 0.5584 (mtm110) cc_final: 0.4795 (mmm160) REVERT: C 334 CYS cc_start: 0.6755 (m) cc_final: 0.5802 (t) REVERT: C 370 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8014 (mttt) REVERT: C 419 GLU cc_start: 0.8081 (tp30) cc_final: 0.7536 (tp30) REVERT: C 421 MET cc_start: 0.7935 (ppp) cc_final: 0.7367 (ppp) outliers start: 32 outliers final: 16 residues processed: 190 average time/residue: 0.5715 time to fit residues: 120.4872 Evaluate side-chains 187 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 108 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126953 restraints weight = 14831.829| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.15 r_work: 0.3586 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14359 Z= 0.121 Angle : 0.521 11.149 19625 Z= 0.271 Chirality : 0.040 0.176 2101 Planarity : 0.004 0.052 2388 Dihedral : 13.880 87.998 2210 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.40 % Allowed : 13.95 % Favored : 83.65 % 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: 1.37 (0.21), residues: 1609 helix: 1.66 (0.20), residues: 704 sheet: 1.08 (0.33), residues: 231 loop : 0.13 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.022 0.002 PHE A 88 TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (14359) covalent geometry : angle 0.52113 / 0.27 (19625) hydrogen bonds : bond 0.03454 / 2.38 ( 675) hydrogen bonds : angle 4.67352 / 3.51 ( 1894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.480 Fit side-chains REVERT: A 177 ARG cc_start: 0.6046 (ttt-90) cc_final: 0.4953 (ttp80) REVERT: A 193 ARG cc_start: 0.7071 (mtm180) cc_final: 0.5139 (mmp80) REVERT: A 263 GLU cc_start: 0.7399 (mp0) cc_final: 0.7093 (mp0) REVERT: A 353 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.6029 (m) REVERT: A 391 ASP cc_start: 0.7163 (m-30) cc_final: 0.6960 (m-30) REVERT: A 459 MET cc_start: 0.8524 (tpp) cc_final: 0.7875 (tmm) REVERT: A 494 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7378 (pm20) REVERT: A 776 ASP cc_start: 0.7970 (t0) cc_final: 0.7714 (t0) REVERT: A 922 GLN cc_start: 0.5914 (mt0) cc_final: 0.5540 (pt0) REVERT: A 1089 GLN cc_start: 0.6996 (mt0) cc_final: 0.6562 (mp10) REVERT: A 1164 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6357 (t80) REVERT: B 123 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: B 134 LYS cc_start: 0.7293 (ttpt) cc_final: 0.5971 (mmtt) REVERT: B 250 GLN cc_start: 0.7213 (mt0) cc_final: 0.6443 (mm-40) REVERT: B 308 ASP cc_start: 0.7472 (p0) cc_final: 0.7087 (p0) REVERT: B 325 ARG cc_start: 0.6200 (mtt90) cc_final: 0.5951 (mtm110) REVERT: C 236 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: C 249 ASN cc_start: 0.5691 (m-40) cc_final: 0.5466 (m110) REVERT: C 325 ARG cc_start: 0.5611 (mtm110) cc_final: 0.4810 (mmm160) REVERT: C 334 CYS cc_start: 0.6715 (m) cc_final: 0.5775 (t) REVERT: C 370 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8003 (mttt) REVERT: C 419 GLU cc_start: 0.8065 (tp30) cc_final: 0.7504 (tp30) REVERT: C 421 MET cc_start: 0.7976 (ppp) cc_final: 0.7410 (ppp) outliers start: 34 outliers final: 17 residues processed: 194 average time/residue: 0.5994 time to fit residues: 127.1208 Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124693 restraints weight = 14820.657| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.14 r_work: 0.3563 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14359 Z= 0.156 Angle : 0.558 12.817 19625 Z= 0.288 Chirality : 0.041 0.181 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.907 87.138 2210 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.11 % Allowed : 14.16 % Favored : 83.72 % 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: 1.20 (0.20), residues: 1609 helix: 1.53 (0.19), residues: 704 sheet: 1.05 (0.33), residues: 216 loop : 0.03 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.024 0.002 PHE B 242 TRP 0.020 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (14359) covalent geometry : angle 0.55776 / 0.29 (19625) hydrogen bonds : bond 0.03793 / 2.62 ( 675) hydrogen bonds : angle 4.75166 / 3.57 ( 1894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.344 Fit side-chains REVERT: A 177 ARG cc_start: 0.6216 (ttt-90) cc_final: 0.5086 (ttp80) REVERT: A 193 ARG cc_start: 0.7202 (mtm180) cc_final: 0.5288 (mmp80) REVERT: A 263 GLU cc_start: 0.7480 (mp0) cc_final: 0.7137 (mp0) REVERT: A 459 MET cc_start: 0.8514 (tpp) cc_final: 0.7861 (tmm) REVERT: A 494 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7460 (pm20) REVERT: A 877 MET cc_start: 0.8000 (tpp) cc_final: 0.7800 (tpp) REVERT: A 922 GLN cc_start: 0.5996 (mt0) cc_final: 0.5580 (pt0) REVERT: A 1089 GLN cc_start: 0.7077 (mt0) cc_final: 0.6671 (mp10) REVERT: A 1164 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6545 (t80) REVERT: B 124 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: B 134 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6067 (mmtt) REVERT: B 250 GLN cc_start: 0.7301 (mt0) cc_final: 0.6608 (mm-40) REVERT: B 314 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6877 (ttp) REVERT: B 325 ARG cc_start: 0.6312 (mtt90) cc_final: 0.5972 (mtm110) REVERT: B 450 ASN cc_start: 0.6720 (p0) cc_final: 0.6447 (p0) REVERT: B 465 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7517 (mpp) REVERT: C 89 ASP cc_start: 0.7219 (t0) cc_final: 0.6896 (m-30) REVERT: C 236 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: C 313 HIS cc_start: 0.5686 (t-90) cc_final: 0.4883 (m90) REVERT: C 325 ARG cc_start: 0.5736 (mtm110) cc_final: 0.4947 (mmm160) REVERT: C 334 CYS cc_start: 0.6877 (m) cc_final: 0.5941 (t) REVERT: C 370 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8060 (mttt) REVERT: C 419 GLU cc_start: 0.8095 (tp30) cc_final: 0.7589 (tp30) REVERT: C 421 MET cc_start: 0.7987 (ppp) cc_final: 0.7546 (ppp) outliers start: 30 outliers final: 19 residues processed: 189 average time/residue: 0.5706 time to fit residues: 117.6741 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 466 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 9 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 0.0370 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.165837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129558 restraints weight = 14785.249| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.98 r_work: 0.3573 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14359 Z= 0.118 Angle : 0.523 9.106 19625 Z= 0.274 Chirality : 0.040 0.169 2101 Planarity : 0.004 0.052 2388 Dihedral : 13.860 86.866 2210 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.40 % Allowed : 14.09 % Favored : 83.51 % 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: 1.31 (0.21), residues: 1609 helix: 1.68 (0.20), residues: 698 sheet: 1.04 (0.33), residues: 223 loop : 0.05 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.023 0.001 TYR A1166 PHE 0.024 0.002 PHE B 242 TRP 0.019 0.001 TRP B 241 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14359) covalent geometry : angle 0.52336 / 0.27 (19625) hydrogen bonds : bond 0.03429 / 2.36 ( 675) hydrogen bonds : angle 4.66580 / 3.50 ( 1894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.468 Fit side-chains REVERT: A 177 ARG cc_start: 0.6146 (ttt-90) cc_final: 0.5075 (ttp80) REVERT: A 193 ARG cc_start: 0.7136 (mtm180) cc_final: 0.5209 (mmp80) REVERT: A 263 GLU cc_start: 0.7450 (mp0) cc_final: 0.7094 (mp0) REVERT: A 459 MET cc_start: 0.8476 (tpp) cc_final: 0.7844 (tmm) REVERT: A 494 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7394 (pm20) REVERT: A 559 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.4993 (mt) REVERT: A 922 GLN cc_start: 0.5793 (mt0) cc_final: 0.5409 (pt0) REVERT: A 1089 GLN cc_start: 0.7076 (mt0) cc_final: 0.6605 (mp10) REVERT: A 1164 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6439 (t80) REVERT: B 123 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: B 134 LYS cc_start: 0.7396 (ttpt) cc_final: 0.6013 (mmtt) REVERT: B 250 GLN cc_start: 0.7235 (mt0) cc_final: 0.6500 (mm-40) REVERT: B 308 ASP cc_start: 0.7543 (p0) cc_final: 0.7285 (p0) REVERT: B 314 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6959 (ttp) REVERT: B 325 ARG cc_start: 0.6311 (mtt90) cc_final: 0.6074 (mtm110) REVERT: B 450 ASN cc_start: 0.6592 (p0) cc_final: 0.6310 (p0) REVERT: B 465 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7422 (mpp) REVERT: C 89 ASP cc_start: 0.7194 (t0) cc_final: 0.6847 (m-30) REVERT: C 191 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7092 (mt-10) REVERT: C 236 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: C 313 HIS cc_start: 0.5652 (t-90) cc_final: 0.4840 (m90) REVERT: C 325 ARG cc_start: 0.5733 (mtm110) cc_final: 0.4947 (mmm160) REVERT: C 334 CYS cc_start: 0.6836 (m) cc_final: 0.5891 (t) REVERT: C 370 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8033 (mttt) REVERT: C 419 GLU cc_start: 0.8047 (tp30) cc_final: 0.7669 (tp30) REVERT: C 421 MET cc_start: 0.7969 (ppp) cc_final: 0.7518 (ppp) outliers start: 34 outliers final: 16 residues processed: 188 average time/residue: 0.5400 time to fit residues: 110.4719 Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.0270 chunk 157 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128257 restraints weight = 14915.845| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.16 r_work: 0.3600 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14359 Z= 0.110 Angle : 0.515 13.203 19625 Z= 0.268 Chirality : 0.039 0.162 2101 Planarity : 0.004 0.053 2388 Dihedral : 13.776 86.191 2210 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.83 % Allowed : 14.87 % Favored : 83.30 % 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: 1.38 (0.21), residues: 1609 helix: 1.77 (0.20), residues: 698 sheet: 1.02 (0.34), residues: 216 loop : 0.09 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.024 0.001 PHE A 273 TRP 0.021 0.001 TRP B 241 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14359) covalent geometry : angle 0.51525 / 0.27 (19625) hydrogen bonds : bond 0.03268 / 2.25 ( 675) hydrogen bonds : angle 4.59447 / 3.45 ( 1894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.564 Fit side-chains REVERT: A 177 ARG cc_start: 0.6039 (ttt-90) cc_final: 0.4980 (ttp80) REVERT: A 263 GLU cc_start: 0.7416 (mp0) cc_final: 0.7152 (mp0) REVERT: A 459 MET cc_start: 0.8469 (tpp) cc_final: 0.7827 (tmm) REVERT: A 494 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7342 (pm20) REVERT: A 922 GLN cc_start: 0.5609 (mt0) cc_final: 0.5249 (pt0) REVERT: A 1089 GLN cc_start: 0.7038 (mt0) cc_final: 0.6558 (mp10) REVERT: A 1164 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6348 (t80) REVERT: B 123 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: B 134 LYS cc_start: 0.7305 (ttpt) cc_final: 0.5920 (mmtt) REVERT: B 250 GLN cc_start: 0.7190 (mt0) cc_final: 0.6417 (mm-40) REVERT: B 308 ASP cc_start: 0.7450 (p0) cc_final: 0.7178 (p0) REVERT: B 325 ARG cc_start: 0.6236 (mtt90) cc_final: 0.6027 (mtm110) REVERT: B 450 ASN cc_start: 0.6459 (p0) cc_final: 0.6192 (p0) REVERT: B 465 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7383 (mpp) REVERT: C 89 ASP cc_start: 0.7170 (t0) cc_final: 0.6801 (m-30) REVERT: C 236 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: C 325 ARG cc_start: 0.5678 (mtm110) cc_final: 0.4890 (mmm160) REVERT: C 334 CYS cc_start: 0.6717 (m) cc_final: 0.5770 (t) REVERT: C 370 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8031 (mttt) REVERT: C 419 GLU cc_start: 0.8048 (tp30) cc_final: 0.7646 (tp30) REVERT: C 421 MET cc_start: 0.8005 (ppp) cc_final: 0.7556 (ppp) outliers start: 26 outliers final: 16 residues processed: 188 average time/residue: 0.5260 time to fit residues: 107.9283 Evaluate side-chains 185 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127724 restraints weight = 14860.821| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.13 r_work: 0.3588 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14359 Z= 0.120 Angle : 0.528 12.831 19625 Z= 0.274 Chirality : 0.040 0.162 2101 Planarity : 0.004 0.054 2388 Dihedral : 13.751 85.738 2210 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.97 % Allowed : 15.43 % Favored : 82.59 % 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: 1.39 (0.21), residues: 1609 helix: 1.77 (0.20), residues: 698 sheet: 1.01 (0.34), residues: 216 loop : 0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.025 0.002 PHE A 273 TRP 0.024 0.001 TRP B 241 HIS 0.003 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14359) covalent geometry : angle 0.52774 / 0.27 (19625) hydrogen bonds : bond 0.03370 / 2.32 ( 675) hydrogen bonds : angle 4.61407 / 3.47 ( 1894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.396 Fit side-chains REVERT: A 177 ARG cc_start: 0.6096 (ttt-90) cc_final: 0.5007 (ttp80) REVERT: A 263 GLU cc_start: 0.7428 (mp0) cc_final: 0.7166 (mp0) REVERT: A 459 MET cc_start: 0.8465 (tpp) cc_final: 0.7842 (tmm) REVERT: A 494 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7316 (pm20) REVERT: A 922 GLN cc_start: 0.5472 (mt0) cc_final: 0.5114 (pt0) REVERT: A 1089 GLN cc_start: 0.7055 (mt0) cc_final: 0.6626 (mp10) REVERT: A 1112 MET cc_start: 0.6707 (tpp) cc_final: 0.6489 (mtt) REVERT: A 1164 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6359 (t80) REVERT: B 123 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: B 124 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: B 134 LYS cc_start: 0.7373 (ttpt) cc_final: 0.5996 (mmtt) REVERT: B 250 GLN cc_start: 0.7202 (mt0) cc_final: 0.6426 (mm-40) REVERT: B 308 ASP cc_start: 0.7490 (p0) cc_final: 0.7203 (p0) REVERT: B 325 ARG cc_start: 0.6255 (mtt90) cc_final: 0.6033 (mtm110) REVERT: B 465 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: C 89 ASP cc_start: 0.7153 (t0) cc_final: 0.6794 (m-30) REVERT: C 236 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: C 325 ARG cc_start: 0.5675 (mtm110) cc_final: 0.4793 (mmm160) REVERT: C 334 CYS cc_start: 0.6734 (m) cc_final: 0.5790 (t) REVERT: C 370 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8039 (mttt) REVERT: C 419 GLU cc_start: 0.8044 (tp30) cc_final: 0.7651 (tp30) REVERT: C 421 MET cc_start: 0.8012 (ppp) cc_final: 0.7647 (ppp) outliers start: 28 outliers final: 17 residues processed: 185 average time/residue: 0.5406 time to fit residues: 108.8805 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 236 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 0.0170 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127691 restraints weight = 14832.002| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.15 r_work: 0.3596 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14359 Z= 0.115 Angle : 0.515 11.606 19625 Z= 0.269 Chirality : 0.039 0.155 2101 Planarity : 0.004 0.053 2388 Dihedral : 13.742 85.559 2210 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.90 % Allowed : 15.22 % Favored : 82.88 % 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: 1.39 (0.21), residues: 1609 helix: 1.77 (0.20), residues: 698 sheet: 1.01 (0.34), residues: 216 loop : 0.11 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.025 0.001 PHE A 273 TRP 0.023 0.001 TRP B 241 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (14359) covalent geometry : angle 0.51483 / 0.27 (19625) hydrogen bonds : bond 0.03316 / 2.28 ( 675) hydrogen bonds : angle 4.60666 / 3.46 ( 1894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.86 seconds wall clock time: 81 minutes 13.29 seconds (4873.29 seconds total)