Starting phenix.real_space_refine on Fri Jul 3 11:25:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ggf_51330/07_2026/9ggf_51330.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ggf_51330/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ggf_51330/07_2026/9ggf_51330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ggf_51330/07_2026/9ggf_51330.map" model { file = "/net/cci-nas-00/data/ceres_data/9ggf_51330/07_2026/9ggf_51330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ggf_51330/07_2026/9ggf_51330.cif" } 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-dev-6108/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.20 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: 1.20 Conformation dependent library (CDL) restraints added in 641.5 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: 1.26 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: 2.65 Time building geometry restraints manager: 1.54 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: 19344 1.80 - 3.61: 258 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 3.250 nonbonded pdb="CA CA A1301 " pdb=" O1B DCP A1302 " model vdw 1.815 3.250 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 3.250 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.450 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- 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 : 0.491 9.015 19625 Z= 0.312 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 0.49099 / 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 : 0.516 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: 0.6466 time to fit residues: 227.5483 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 : 0.518 ------------------------------------------------------------------------------- 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 ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4000 r_free = 0.4000 target = 0.164141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125281 restraints weight = 14883.439| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.16 r_work: 0.3554 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14359 Z= 0.234 Angle : 0.658 10.834 19625 Z= 0.340 Chirality : 0.045 0.177 2101 Planarity : 0.006 0.050 2388 Dihedral : 14.122 107.664 2213 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.10 % Allowed : 11.28 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1609 helix: 1.26 (0.19), residues: 704 sheet: 0.97 (0.32), residues: 237 loop : 0.04 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 275 TYR 0.019 0.003 TYR B 291 PHE 0.021 0.002 PHE A1129 TRP 0.016 0.002 TRP B 241 HIS 0.006 0.001 HIS A 911 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (14359) covalent geometry : angle 0.65829 / 0.34 (19625) hydrogen bonds : bond 0.04902 / 3.35 ( 675) hydrogen bonds : angle 5.26924 / 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 235 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 158 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6564 (mm) REVERT: A 177 ARG cc_start: 0.6087 (ttt-90) cc_final: 0.5047 (ttp80) REVERT: A 193 ARG cc_start: 0.7184 (mtm180) cc_final: 0.5146 (mmp80) REVERT: A 232 ARG cc_start: 0.6273 (mtt180) cc_final: 0.5398 (mtm180) REVERT: A 263 GLU cc_start: 0.7419 (mp0) cc_final: 0.6841 (mp0) REVERT: A 459 MET cc_start: 0.8538 (tpp) cc_final: 0.7856 (tmm) REVERT: A 603 MET cc_start: 0.8405 (mtt) cc_final: 0.8204 (mtt) REVERT: A 773 LYS cc_start: 0.7308 (mmmt) cc_final: 0.6491 (mppt) REVERT: A 1089 GLN cc_start: 0.7119 (mt0) cc_final: 0.6644 (mp10) REVERT: B 134 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6170 (mmtt) REVERT: B 250 GLN cc_start: 0.7343 (mt0) cc_final: 0.6521 (mm-40) REVERT: B 325 ARG cc_start: 0.6089 (mtt90) cc_final: 0.5740 (mtm110) REVERT: C 236 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: C 249 ASN cc_start: 0.5684 (m-40) cc_final: 0.5409 (m110) REVERT: C 334 CYS cc_start: 0.6859 (m) cc_final: 0.5971 (t) REVERT: C 370 LYS cc_start: 0.8299 (mmtm) cc_final: 0.8033 (mttt) REVERT: C 407 LEU cc_start: 0.7439 (mt) cc_final: 0.7228 (mm) outliers start: 44 outliers final: 16 residues processed: 213 average time/residue: 0.6634 time to fit residues: 153.8563 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 : 0.630 ------------------------------------------------------------------------------- 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: 2.9990 chunk 146 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.164920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.126604 restraints weight = 14877.882| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.12 r_work: 0.3571 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14359 Z= 0.150 Angle : 0.553 10.409 19625 Z= 0.289 Chirality : 0.041 0.155 2101 Planarity : 0.005 0.050 2388 Dihedral : 13.905 89.205 2212 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.18 % Allowed : 12.90 % Favored : 84.92 % 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: 1.18 (0.21), residues: 1609 helix: 1.42 (0.20), residues: 704 sheet: 1.07 (0.32), residues: 237 loop : 0.10 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1071 TYR 0.020 0.002 TYR A1166 PHE 0.020 0.002 PHE A 88 TRP 0.016 0.001 TRP B 241 HIS 0.004 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (14359) covalent geometry : angle 0.55270 / 0.29 (19625) hydrogen bonds : bond 0.04008 / 2.74 ( 675) hydrogen bonds : angle 4.97011 / 3.70 ( 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 208 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.517 Fit side-chains REVERT: A 177 ARG cc_start: 0.6098 (ttt-90) cc_final: 0.5063 (ttp80) REVERT: A 193 ARG cc_start: 0.7170 (mtm180) cc_final: 0.5164 (mmp80) REVERT: A 232 ARG cc_start: 0.6331 (mtt180) cc_final: 0.5513 (mtm180) REVERT: A 263 GLU cc_start: 0.7411 (mp0) cc_final: 0.7124 (mp0) REVERT: A 459 MET cc_start: 0.8510 (tpp) cc_final: 0.7862 (tmm) REVERT: A 494 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7504 (pm20) REVERT: A 773 LYS cc_start: 0.7442 (mmmt) cc_final: 0.6615 (mppt) REVERT: A 776 ASP cc_start: 0.7973 (t0) cc_final: 0.7676 (t0) REVERT: A 1089 GLN cc_start: 0.7114 (mt0) cc_final: 0.6626 (mp10) REVERT: B 134 LYS cc_start: 0.7421 (ttpt) cc_final: 0.6258 (mmtt) REVERT: B 250 GLN cc_start: 0.7411 (mt0) cc_final: 0.6688 (mm-40) REVERT: B 308 ASP cc_start: 0.7491 (p0) cc_final: 0.7194 (p0) REVERT: B 325 ARG cc_start: 0.6208 (mtt90) cc_final: 0.5906 (mtm110) REVERT: C 236 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: C 249 ASN cc_start: 0.5812 (m-40) cc_final: 0.5585 (m110) REVERT: C 325 ARG cc_start: 0.5582 (mtm110) cc_final: 0.4853 (mmm160) REVERT: C 334 CYS cc_start: 0.6932 (m) cc_final: 0.6000 (t) REVERT: C 370 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8070 (mttt) REVERT: C 419 GLU cc_start: 0.8097 (tp30) cc_final: 0.7669 (tp30) REVERT: C 421 MET cc_start: 0.7863 (ppp) cc_final: 0.7452 (ppp) outliers start: 31 outliers final: 17 residues processed: 193 average time/residue: 0.6322 time to fit residues: 132.9834 Evaluate side-chains 184 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 1141 VAL 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 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: 6.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126219 restraints weight = 14873.479| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.13 r_work: 0.3573 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14359 Z= 0.141 Angle : 0.542 10.145 19625 Z= 0.283 Chirality : 0.041 0.157 2101 Planarity : 0.005 0.052 2388 Dihedral : 13.904 89.810 2210 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.75 % Allowed : 12.83 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1609 helix: 1.52 (0.20), residues: 703 sheet: 0.87 (0.31), residues: 247 loop : 0.11 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.021 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 0.00319 / 0.14 (14359) covalent geometry : angle 0.54182 / 0.28 (19625) hydrogen bonds : bond 0.03759 / 2.58 ( 675) hydrogen bonds : angle 4.84167 / 3.62 ( 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 216 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.347 Fit side-chains REVERT: A 177 ARG cc_start: 0.6016 (ttt-90) cc_final: 0.4966 (ttp80) REVERT: A 193 ARG cc_start: 0.7120 (mtm180) cc_final: 0.5180 (mmp80) REVERT: A 232 ARG cc_start: 0.6269 (mtt180) cc_final: 0.5591 (mtm180) REVERT: A 263 GLU cc_start: 0.7409 (mp0) cc_final: 0.7132 (mp0) REVERT: A 459 MET cc_start: 0.8515 (tpp) cc_final: 0.7871 (tmm) REVERT: A 494 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7475 (pm20) REVERT: A 559 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5070 (mt) REVERT: A 773 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6552 (mppt) REVERT: A 776 ASP cc_start: 0.7968 (t0) cc_final: 0.7665 (t0) REVERT: A 922 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.5885 (mt0) REVERT: A 1089 GLN cc_start: 0.7005 (mt0) cc_final: 0.6594 (mp10) REVERT: B 134 LYS cc_start: 0.7415 (ttpt) cc_final: 0.6162 (mmtt) REVERT: B 250 GLN cc_start: 0.7390 (mt0) cc_final: 0.6662 (mm-40) REVERT: B 308 ASP cc_start: 0.7484 (p0) cc_final: 0.7143 (p0) REVERT: B 325 ARG cc_start: 0.6196 (mtt90) cc_final: 0.5933 (mtm110) REVERT: C 183 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: C 236 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: C 249 ASN cc_start: 0.5785 (m-40) cc_final: 0.5556 (m110) REVERT: C 325 ARG cc_start: 0.5610 (mtm110) cc_final: 0.4841 (mmm160) REVERT: C 334 CYS cc_start: 0.6865 (m) cc_final: 0.5936 (t) REVERT: C 370 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8051 (mttt) REVERT: C 419 GLU cc_start: 0.8070 (tp30) cc_final: 0.7580 (tp30) REVERT: C 421 MET cc_start: 0.7989 (ppp) cc_final: 0.7453 (ppp) outliers start: 39 outliers final: 18 residues processed: 200 average time/residue: 0.5806 time to fit residues: 126.8270 Evaluate side-chains 192 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 416 GLU 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 1121 GLU Chi-restraints excluded: chain A residue 1141 VAL 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 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: 3.9990 chunk 160 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN A 906 HIS ** 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 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 = 0.3975 r_free = 0.3975 target = 0.161665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122686 restraints weight = 14885.833| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.15 r_work: 0.3541 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14359 Z= 0.234 Angle : 0.641 10.707 19625 Z= 0.328 Chirality : 0.045 0.179 2101 Planarity : 0.006 0.059 2388 Dihedral : 14.023 88.441 2210 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.61 % Allowed : 13.88 % 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: 0.90 (0.20), residues: 1609 helix: 1.18 (0.19), residues: 703 sheet: 0.92 (0.32), residues: 231 loop : -0.03 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.022 0.002 PHE B 242 TRP 0.019 0.002 TRP B 241 HIS 0.007 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (14359) covalent geometry : angle 0.64120 / 0.33 (19625) hydrogen bonds : bond 0.04482 / 3.09 ( 675) hydrogen bonds : angle 5.01792 / 3.76 ( 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 215 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.653 Fit side-chains REVERT: A 177 ARG cc_start: 0.6112 (ttt-90) cc_final: 0.4982 (ttp80) REVERT: A 193 ARG cc_start: 0.7185 (mtm180) cc_final: 0.5235 (mmp80) REVERT: A 263 GLU cc_start: 0.7462 (mp0) cc_final: 0.7107 (mp0) REVERT: A 459 MET cc_start: 0.8503 (tpp) cc_final: 0.7834 (tmm) REVERT: A 494 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7424 (pm20) REVERT: A 559 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.4989 (mt) REVERT: A 776 ASP cc_start: 0.8005 (t0) cc_final: 0.7711 (t0) REVERT: A 793 GLU cc_start: 0.6482 (mt-10) cc_final: 0.6208 (tt0) REVERT: A 1089 GLN cc_start: 0.7011 (mt0) cc_final: 0.6565 (mp10) REVERT: B 124 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: B 134 LYS cc_start: 0.7310 (ttpt) cc_final: 0.5931 (mmtt) REVERT: B 250 GLN cc_start: 0.7362 (mt0) cc_final: 0.6592 (mm-40) REVERT: B 325 ARG cc_start: 0.6154 (mtt90) cc_final: 0.5824 (mtm110) REVERT: C 236 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: C 313 HIS cc_start: 0.5586 (t-90) cc_final: 0.4757 (m90) REVERT: C 325 ARG cc_start: 0.5602 (mtm110) cc_final: 0.4814 (mmm160) REVERT: C 334 CYS cc_start: 0.6799 (m) cc_final: 0.5854 (t) REVERT: C 370 LYS cc_start: 0.8365 (mmtm) cc_final: 0.8040 (mttt) REVERT: C 419 GLU cc_start: 0.8154 (tp30) cc_final: 0.7630 (tp30) REVERT: C 421 MET cc_start: 0.8067 (ppp) cc_final: 0.7486 (ppp) outliers start: 37 outliers final: 17 residues processed: 202 average time/residue: 0.6650 time to fit residues: 146.4401 Evaluate side-chains 192 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 416 GLU 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 1053 THR Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 110 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 163 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.164415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125708 restraints weight = 14814.535| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.13 r_work: 0.3566 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2477 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= 0.130 Angle : 0.542 11.176 19625 Z= 0.282 Chirality : 0.040 0.182 2101 Planarity : 0.005 0.053 2388 Dihedral : 13.991 88.403 2210 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.40 % Allowed : 14.59 % Favored : 83.02 % 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: 1.15 (0.21), residues: 1609 helix: 1.49 (0.20), residues: 702 sheet: 0.95 (0.32), residues: 238 loop : 0.02 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.021 0.002 TYR A1166 PHE 0.022 0.002 PHE A 88 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 0.00289 / 0.13 (14359) covalent geometry : angle 0.54243 / 0.28 (19625) hydrogen bonds : bond 0.03652 / 2.52 ( 675) hydrogen bonds : angle 4.79689 / 3.60 ( 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 202 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.537 Fit side-chains REVERT: A 177 ARG cc_start: 0.6151 (ttt-90) cc_final: 0.4999 (ttp80) REVERT: A 263 GLU cc_start: 0.7436 (mp0) cc_final: 0.7195 (mp0) REVERT: A 459 MET cc_start: 0.8462 (tpp) cc_final: 0.7820 (tmm) REVERT: A 494 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: A 776 ASP cc_start: 0.7984 (t0) cc_final: 0.7717 (t0) REVERT: A 922 GLN cc_start: 0.5868 (mt0) cc_final: 0.5445 (pt0) REVERT: A 1089 GLN cc_start: 0.6991 (mt0) cc_final: 0.6586 (mp10) REVERT: A 1164 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6396 (t80) REVERT: B 134 LYS cc_start: 0.7307 (ttpt) cc_final: 0.5928 (mmtt) REVERT: B 250 GLN cc_start: 0.7209 (mt0) cc_final: 0.6448 (mm-40) REVERT: B 308 ASP cc_start: 0.7576 (p0) cc_final: 0.7289 (p0) REVERT: B 325 ARG cc_start: 0.6233 (mtt90) cc_final: 0.5942 (mtm110) REVERT: B 465 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (mpp) REVERT: C 89 ASP cc_start: 0.7129 (t0) cc_final: 0.6791 (m-30) REVERT: C 183 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: C 236 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7255 (mt-10) REVERT: C 313 HIS cc_start: 0.5342 (t-90) cc_final: 0.4545 (m90) REVERT: C 325 ARG cc_start: 0.5637 (mtm110) cc_final: 0.4818 (mmm160) REVERT: C 334 CYS cc_start: 0.6775 (m) cc_final: 0.5831 (t) REVERT: C 370 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8020 (mttt) REVERT: C 419 GLU cc_start: 0.8153 (tp30) cc_final: 0.7641 (tp30) REVERT: C 421 MET cc_start: 0.8010 (ppp) cc_final: 0.7558 (ppp) outliers start: 34 outliers final: 15 residues processed: 187 average time/residue: 0.6291 time to fit residues: 128.6222 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 : 0.440 ------------------------------------------------------------------------------- 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 454 GLU Chi-restraints excluded: chain A residue 494 GLU 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 1141 VAL 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 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 183 GLU Chi-restraints excluded: chain C residue 236 GLU 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: 7.9990 chunk 150 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** 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 = 0.4011 r_free = 0.4011 target = 0.165001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126411 restraints weight = 14809.652| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.12 r_work: 0.3575 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14359 Z= 0.126 Angle : 0.527 12.320 19625 Z= 0.275 Chirality : 0.040 0.182 2101 Planarity : 0.005 0.053 2388 Dihedral : 13.908 87.677 2210 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.18 % Allowed : 14.80 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1609 helix: 1.59 (0.20), residues: 702 sheet: 1.06 (0.34), residues: 216 loop : 0.01 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.022 0.002 PHE B 242 TRP 0.020 0.001 TRP B 241 HIS 0.004 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14359) covalent geometry : angle 0.52660 / 0.27 (19625) hydrogen bonds : bond 0.03529 / 2.43 ( 675) hydrogen bonds : angle 4.70762 / 3.54 ( 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 203 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.544 Fit side-chains REVERT: A 177 ARG cc_start: 0.6167 (ttt-90) cc_final: 0.5032 (ttp80) REVERT: A 263 GLU cc_start: 0.7455 (mp0) cc_final: 0.7201 (mp0) REVERT: A 459 MET cc_start: 0.8506 (tpp) cc_final: 0.7875 (tmm) REVERT: A 494 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: A 922 GLN cc_start: 0.6109 (mt0) cc_final: 0.5733 (pt0) REVERT: A 1089 GLN cc_start: 0.7059 (mt0) cc_final: 0.6610 (mp10) REVERT: A 1164 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6458 (t80) REVERT: B 124 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: B 134 LYS cc_start: 0.7395 (ttpt) cc_final: 0.6030 (mmtt) REVERT: B 250 GLN cc_start: 0.7283 (mt0) cc_final: 0.6565 (mm-40) REVERT: B 308 ASP cc_start: 0.7521 (p0) cc_final: 0.7227 (p0) REVERT: B 325 ARG cc_start: 0.6320 (mtt90) cc_final: 0.6098 (mtm110) REVERT: C 89 ASP cc_start: 0.7190 (t0) cc_final: 0.6877 (m-30) REVERT: C 236 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: C 325 ARG cc_start: 0.5726 (mtm110) cc_final: 0.4825 (mmm160) REVERT: C 334 CYS cc_start: 0.6822 (m) cc_final: 0.5863 (t) REVERT: C 370 LYS cc_start: 0.8349 (mmtm) cc_final: 0.8057 (mttt) REVERT: C 419 GLU cc_start: 0.8104 (tp30) cc_final: 0.7635 (tp30) REVERT: C 421 MET cc_start: 0.7977 (ppp) cc_final: 0.7510 (ppp) outliers start: 31 outliers final: 15 residues processed: 190 average time/residue: 0.5950 time to fit residues: 123.6216 Evaluate side-chains 186 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 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 494 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 9 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.164223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125511 restraints weight = 14773.473| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.13 r_work: 0.3565 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2604 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= 0.155 Angle : 0.564 13.115 19625 Z= 0.291 Chirality : 0.041 0.166 2101 Planarity : 0.005 0.053 2388 Dihedral : 13.903 87.146 2210 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.26 % Allowed : 14.80 % Favored : 82.95 % 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: 1.14 (0.20), residues: 1609 helix: 1.47 (0.19), residues: 704 sheet: 0.99 (0.33), residues: 224 loop : 0.01 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1071 TYR 0.022 0.002 TYR A1166 PHE 0.037 0.002 PHE A1120 TRP 0.020 0.001 TRP B 241 HIS 0.006 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (14359) covalent geometry : angle 0.56402 / 0.29 (19625) hydrogen bonds : bond 0.03766 / 2.60 ( 675) hydrogen bonds : angle 4.76785 / 3.58 ( 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 203 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.529 Fit side-chains REVERT: A 177 ARG cc_start: 0.6144 (ttt-90) cc_final: 0.5044 (ttp80) REVERT: A 263 GLU cc_start: 0.7448 (mp0) cc_final: 0.7182 (mp0) REVERT: A 459 MET cc_start: 0.8481 (tpp) cc_final: 0.7832 (tmm) REVERT: A 494 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: A 922 GLN cc_start: 0.5928 (mt0) cc_final: 0.5556 (pt0) REVERT: A 1089 GLN cc_start: 0.7060 (mt0) cc_final: 0.6627 (mp10) REVERT: A 1164 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6400 (t80) REVERT: B 124 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: B 134 LYS cc_start: 0.7355 (ttpt) cc_final: 0.5942 (mmtt) REVERT: B 250 GLN cc_start: 0.7236 (mt0) cc_final: 0.6463 (mm-40) REVERT: B 306 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6122 (mt) REVERT: B 308 ASP cc_start: 0.7525 (p0) cc_final: 0.7188 (p0) REVERT: B 314 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6815 (ttp) REVERT: B 325 ARG cc_start: 0.6261 (mtt90) cc_final: 0.5977 (mtm110) REVERT: C 89 ASP cc_start: 0.7119 (t0) cc_final: 0.6790 (m-30) REVERT: C 236 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: C 313 HIS cc_start: 0.5349 (t-90) cc_final: 0.4553 (m90) REVERT: C 325 ARG cc_start: 0.5664 (mtm110) cc_final: 0.4770 (mmm160) REVERT: C 334 CYS cc_start: 0.6789 (m) cc_final: 0.5822 (t) REVERT: C 370 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8034 (mttt) REVERT: C 419 GLU cc_start: 0.8126 (tp30) cc_final: 0.7632 (tp30) REVERT: C 421 MET cc_start: 0.7995 (ppp) cc_final: 0.7618 (ppp) outliers start: 32 outliers final: 17 residues processed: 190 average time/residue: 0.5553 time to fit residues: 115.1662 Evaluate side-chains 189 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 494 GLU 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 910 MET Chi-restraints excluded: chain A residue 1141 VAL 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 306 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 157 optimal weight: 0.0370 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.166257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127718 restraints weight = 14891.957| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.13 r_work: 0.3585 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14359 Z= 0.114 Angle : 0.519 8.862 19625 Z= 0.272 Chirality : 0.039 0.175 2101 Planarity : 0.004 0.054 2388 Dihedral : 13.859 86.804 2210 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.62 % Allowed : 15.50 % 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: 1.28 (0.21), residues: 1609 helix: 1.68 (0.20), residues: 697 sheet: 0.99 (0.34), residues: 216 loop : 0.03 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.027 0.002 PHE A1120 TRP 0.021 0.001 TRP B 241 HIS 0.003 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14359) covalent geometry : angle 0.51908 / 0.27 (19625) hydrogen bonds : bond 0.03359 / 2.31 ( 675) hydrogen bonds : angle 4.65556 / 3.50 ( 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 190 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.481 Fit side-chains REVERT: A 177 ARG cc_start: 0.6049 (ttt-90) cc_final: 0.4947 (ttp80) REVERT: A 263 GLU cc_start: 0.7460 (mp0) cc_final: 0.7241 (mp0) REVERT: A 459 MET cc_start: 0.8455 (tpp) cc_final: 0.7829 (tmm) REVERT: A 494 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: A 559 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.4962 (mt) REVERT: A 922 GLN cc_start: 0.5837 (mt0) cc_final: 0.5501 (pt0) REVERT: A 1089 GLN cc_start: 0.7075 (mt0) cc_final: 0.6575 (mp10) REVERT: A 1164 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6351 (t80) REVERT: B 123 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: B 134 LYS cc_start: 0.7335 (ttpt) cc_final: 0.5938 (mmtt) REVERT: B 250 GLN cc_start: 0.7228 (mt0) cc_final: 0.6468 (mm-40) REVERT: B 306 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6016 (mt) REVERT: B 308 ASP cc_start: 0.7490 (p0) cc_final: 0.7171 (p0) REVERT: B 314 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6885 (ttp) REVERT: B 465 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7382 (mpp) REVERT: C 89 ASP cc_start: 0.7161 (t0) cc_final: 0.6815 (m-30) REVERT: C 236 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: C 325 ARG cc_start: 0.5635 (mtm110) cc_final: 0.4779 (mmm160) REVERT: C 334 CYS cc_start: 0.6749 (m) cc_final: 0.5799 (t) REVERT: C 370 LYS cc_start: 0.8378 (mmtm) cc_final: 0.8054 (mttt) REVERT: C 419 GLU cc_start: 0.8098 (tp30) cc_final: 0.7619 (tp30) REVERT: C 421 MET cc_start: 0.8007 (ppp) cc_final: 0.7645 (ppp) outliers start: 23 outliers final: 10 residues processed: 179 average time/residue: 0.5989 time to fit residues: 116.8744 Evaluate side-chains 180 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 494 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 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 306 LEU 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 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: 6.9990 chunk 147 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 60 optimal weight: 0.0970 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.167152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128723 restraints weight = 14844.537| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.12 r_work: 0.3597 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14359 Z= 0.110 Angle : 0.516 13.433 19625 Z= 0.268 Chirality : 0.039 0.154 2101 Planarity : 0.004 0.055 2388 Dihedral : 13.786 86.201 2210 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.69 % Allowed : 15.79 % Favored : 82.52 % 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: 1.35 (0.21), residues: 1609 helix: 1.73 (0.20), residues: 697 sheet: 1.04 (0.34), residues: 216 loop : 0.08 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1071 TYR 0.022 0.001 TYR A1166 PHE 0.029 0.002 PHE A1120 TRP 0.024 0.001 TRP B 241 HIS 0.003 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (14359) covalent geometry : angle 0.51566 / 0.27 (19625) hydrogen bonds : bond 0.03311 / 2.28 ( 675) hydrogen bonds : angle 4.60966 / 3.46 ( 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 194 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.468 Fit side-chains REVERT: A 177 ARG cc_start: 0.6066 (ttt-90) cc_final: 0.4957 (ttp80) REVERT: A 263 GLU cc_start: 0.7438 (mp0) cc_final: 0.7220 (mp0) REVERT: A 459 MET cc_start: 0.8482 (tpp) cc_final: 0.7862 (tmm) REVERT: A 494 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: A 922 GLN cc_start: 0.5643 (mt0) cc_final: 0.5328 (pt0) REVERT: A 1089 GLN cc_start: 0.7050 (mt0) cc_final: 0.6567 (mp10) REVERT: A 1164 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6340 (t80) REVERT: B 123 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: B 134 LYS cc_start: 0.7342 (ttpt) cc_final: 0.5940 (mmtt) REVERT: B 250 GLN cc_start: 0.7221 (mt0) cc_final: 0.6459 (mm-40) REVERT: B 306 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.5919 (mt) REVERT: B 308 ASP cc_start: 0.7489 (p0) cc_final: 0.7165 (p0) REVERT: B 325 ARG cc_start: 0.6213 (mtm110) cc_final: 0.5932 (mtm110) REVERT: B 465 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7330 (mpp) REVERT: C 89 ASP cc_start: 0.7157 (t0) cc_final: 0.6810 (m-30) REVERT: C 236 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: C 325 ARG cc_start: 0.5680 (mtm110) cc_final: 0.4811 (mmm160) REVERT: C 334 CYS cc_start: 0.6784 (m) cc_final: 0.5820 (t) REVERT: C 370 LYS cc_start: 0.8371 (mmtm) cc_final: 0.8071 (mttt) REVERT: C 419 GLU cc_start: 0.8107 (tp30) cc_final: 0.7635 (tp30) REVERT: C 421 MET cc_start: 0.8011 (ppp) cc_final: 0.7659 (ppp) outliers start: 24 outliers final: 11 residues processed: 184 average time/residue: 0.5728 time to fit residues: 115.1015 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 494 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 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 306 LEU Chi-restraints excluded: chain B residue 371 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 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: 4.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 736 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125692 restraints weight = 14828.095| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.13 r_work: 0.3568 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14359 Z= 0.151 Angle : 0.568 12.804 19625 Z= 0.292 Chirality : 0.041 0.159 2101 Planarity : 0.005 0.054 2388 Dihedral : 13.809 85.816 2210 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.76 % Allowed : 15.79 % Favored : 82.45 % 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: 1.21 (0.20), residues: 1609 helix: 1.58 (0.20), residues: 698 sheet: 0.99 (0.33), residues: 216 loop : 0.04 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.025 0.002 TYR B 432 PHE 0.029 0.002 PHE A1120 TRP 0.027 0.001 TRP B 241 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (14359) covalent geometry : angle 0.56830 / 0.29 (19625) hydrogen bonds : bond 0.03719 / 2.56 ( 675) hydrogen bonds : angle 4.71794 / 3.54 ( 1894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.43 seconds wall clock time: 86 minutes 49.86 seconds (5209.86 seconds total)