Starting phenix.real_space_refine on Wed Apr 30 23:06:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.map" model { file = "/net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iza_35837/04_2025/8iza_35837.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 P 6 5.49 5 Mg 2 5.21 5 S 45 5.16 5 C 6448 2.51 5 N 1684 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9985 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1246, 9921 Classifications: {'peptide': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1205} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.42, per 1000 atoms: 0.64 Number of scatterers: 9985 At special positions: 0 Unit cell: (82.935, 91.485, 154.755, 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) S 45 16.00 P 6 15.00 Mg 2 11.99 O 1800 8.00 N 1684 7.00 C 6448 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 67.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.912A pdb=" N PHE A 23 " --> pdb=" O CYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.735A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.892A pdb=" N MET A 44 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.660A pdb=" N GLU A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 89 removed outlier: 4.149A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 4.492A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.726A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.840A pdb=" N ILE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 150 Processing helix chain 'A' and resid 150 through 179 removed outlier: 4.124A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.576A pdb=" N GLY A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.672A pdb=" N ILE A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 231 removed outlier: 3.603A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.577A pdb=" N MET A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 237 through 275 removed outlier: 3.860A pdb=" N MET A 241 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.726A pdb=" N GLY A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 257 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 291 through 334 removed outlier: 3.688A pdb=" N LEU A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.544A pdb=" N LEU A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 391 removed outlier: 3.977A pdb=" N ALA A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.546A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 removed outlier: 3.877A pdb=" N LEU A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 removed outlier: 4.183A pdb=" N LYS A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.510A pdb=" N LEU A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 removed outlier: 3.502A pdb=" N LEU A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 525' Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.537A pdb=" N GLY A 532 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.525A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.825A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 572 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.982A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 599 " --> pdb=" O TYR A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 599' Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.983A pdb=" N PHE A 620 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.725A pdb=" N ASN A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 751 removed outlier: 3.546A pdb=" N ILE A 718 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.898A pdb=" N LYS A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.889A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.598A pdb=" N ILE A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 858 removed outlier: 3.608A pdb=" N ASP A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 918 removed outlier: 3.601A pdb=" N LEU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.673A pdb=" N SER A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 966 removed outlier: 3.572A pdb=" N HIS A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 Processing helix chain 'A' and resid 981 through 1015 removed outlier: 3.866A pdb=" N ARG A1012 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A1013 " --> pdb=" O SER A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1080 through 1090 removed outlier: 3.798A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.827A pdb=" N ILE A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1154 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1178 through 1194 removed outlier: 3.755A pdb=" N LYS A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 3.765A pdb=" N THR A1237 " --> pdb=" O ARG A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1263 Processing helix chain 'A' and resid 1267 through 1274 Processing helix chain 'A' and resid 1278 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 431 through 435 removed outlier: 5.826A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 412 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 470 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP A 414 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 468 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.635A pdb=" N VAL A 590 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.668A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1065 removed outlier: 5.160A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 7.247A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A1073 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A1256 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A1254 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP A1248 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3163 1.35 - 1.46: 2331 1.46 - 1.58: 4623 1.58 - 1.69: 10 1.69 - 1.81: 72 Bond restraints: 10199 Sorted by residual: bond pdb=" C4 ATP A1402 " pdb=" C5 ATP A1402 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP A1401 " pdb=" C5 ATP A1401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C5 ATP A1401 " pdb=" C6 ATP A1401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C5 ATP A1402 " pdb=" C6 ATP A1402 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C8 ATP A1402 " pdb=" N7 ATP A1402 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.26e+01 ... (remaining 10194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 13798 3.90 - 7.79: 31 7.79 - 11.69: 6 11.69 - 15.58: 0 15.58 - 19.48: 4 Bond angle restraints: 13839 Sorted by residual: angle pdb=" PB ATP A1401 " pdb=" O3B ATP A1401 " pdb=" PG ATP A1401 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP A1402 " pdb=" O3B ATP A1402 " pdb=" PG ATP A1402 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PA ATP A1402 " pdb=" O3A ATP A1402 " pdb=" PB ATP A1402 " ideal model delta sigma weight residual 136.83 119.78 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP A1401 " pdb=" O3A ATP A1401 " pdb=" PB ATP A1401 " ideal model delta sigma weight residual 136.83 120.69 16.14 1.00e+00 1.00e+00 2.61e+02 angle pdb=" C5 ATP A1402 " pdb=" C4 ATP A1402 " pdb=" N3 ATP A1402 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.65e+01 ... (remaining 13834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 5609 17.50 - 35.01: 424 35.01 - 52.51: 66 52.51 - 70.02: 15 70.02 - 87.52: 9 Dihedral angle restraints: 6123 sinusoidal: 2489 harmonic: 3634 Sorted by residual: dihedral pdb=" CA ASP A 74 " pdb=" CB ASP A 74 " pdb=" CG ASP A 74 " pdb=" OD1 ASP A 74 " ideal model delta sinusoidal sigma weight residual -30.00 -89.08 59.08 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ALA A 348 " pdb=" C ALA A 348 " pdb=" N SER A 349 " pdb=" CA SER A 349 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A1038 " pdb=" CG GLU A1038 " pdb=" CD GLU A1038 " pdb=" OE1 GLU A1038 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 982 0.026 - 0.052: 387 0.052 - 0.079: 151 0.079 - 0.105: 51 0.105 - 0.131: 30 Chirality restraints: 1601 Sorted by residual: chirality pdb=" CA ILE A1120 " pdb=" N ILE A1120 " pdb=" C ILE A1120 " pdb=" CB ILE A1120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" C1' ATP A1402 " pdb=" C2' ATP A1402 " pdb=" N9 ATP A1402 " pdb=" O4' ATP A1402 " both_signs ideal model delta sigma weight residual False 2.41 2.54 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1598 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 335 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C THR A 335 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 335 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 336 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 248 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO A 249 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 109 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 110 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " 0.015 5.00e-02 4.00e+02 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 112 2.67 - 3.23: 9424 3.23 - 3.79: 15218 3.79 - 4.34: 19505 4.34 - 4.90: 32695 Nonbonded interactions: 76954 Sorted by model distance: nonbonded pdb=" O2B ATP A1401 " pdb="MG MG A1403 " model vdw 2.116 2.170 nonbonded pdb=" OE1 GLN A 480 " pdb="MG MG A1403 " model vdw 2.119 2.170 nonbonded pdb=" O2B ATP A1402 " pdb="MG MG A1404 " model vdw 2.157 2.170 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.226 3.040 nonbonded pdb=" O ASP A 842 " pdb=" OG1 THR A 846 " model vdw 2.284 3.040 ... (remaining 76949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.083 10199 Z= 0.232 Angle : 0.607 19.480 13839 Z= 0.456 Chirality : 0.037 0.131 1601 Planarity : 0.003 0.028 1715 Dihedral : 12.639 87.524 3771 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.22), residues: 1242 helix: -0.19 (0.18), residues: 758 sheet: -1.28 (0.67), residues: 53 loop : -2.55 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP A 216 HIS 0.001 0.000 HIS A 153 PHE 0.011 0.001 PHE A 993 TYR 0.008 0.001 TYR A 985 ARG 0.001 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.12333 ( 570) hydrogen bonds : angle 4.31441 ( 1683) covalent geometry : bond 0.00282 (10199) covalent geometry : angle 0.60684 (13839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.9082 (mmt) cc_final: 0.8862 (mmt) REVERT: A 899 PRO cc_start: 0.8222 (Cg_exo) cc_final: 0.8016 (Cg_endo) REVERT: A 1007 MET cc_start: 0.8764 (mmm) cc_final: 0.8482 (mmm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3549 time to fit residues: 111.8650 Evaluate side-chains 130 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 153 HIS A 172 HIS A 183 ASN A 472 HIS A 721 ASN A 750 ASN A 931 GLN A1176 ASN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 GLN A1233 HIS A1236 ASN A1274 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115730 restraints weight = 16930.496| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.10 r_work: 0.3396 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10199 Z= 0.148 Angle : 0.553 7.835 13839 Z= 0.284 Chirality : 0.040 0.170 1601 Planarity : 0.003 0.029 1715 Dihedral : 5.863 78.246 1412 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.03 % Allowed : 9.95 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1242 helix: 0.92 (0.19), residues: 765 sheet: -1.64 (0.59), residues: 68 loop : -1.91 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 483 HIS 0.006 0.001 HIS A 472 PHE 0.030 0.002 PHE A 993 TYR 0.015 0.001 TYR A 477 ARG 0.006 0.001 ARG A 706 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 570) hydrogen bonds : angle 3.61870 ( 1683) covalent geometry : bond 0.00336 (10199) covalent geometry : angle 0.55272 (13839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7747 (tt0) REVERT: A 297 ASN cc_start: 0.8086 (m-40) cc_final: 0.7502 (t0) REVERT: A 468 LEU cc_start: 0.8461 (pt) cc_final: 0.8152 (pp) REVERT: A 744 MET cc_start: 0.6283 (tmm) cc_final: 0.6002 (tmm) REVERT: A 828 ASP cc_start: 0.8907 (m-30) cc_final: 0.8318 (m-30) REVERT: A 842 ASP cc_start: 0.8784 (t0) cc_final: 0.8182 (t0) REVERT: A 950 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 1272 MET cc_start: 0.8848 (ptp) cc_final: 0.8526 (ptm) REVERT: A 1280 GLU cc_start: 0.7851 (tp30) cc_final: 0.7643 (tp30) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.2073 time to fit residues: 48.0904 Evaluate side-chains 126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1198 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 78 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 HIS ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.130345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100079 restraints weight = 17198.615| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.07 r_work: 0.3174 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10199 Z= 0.159 Angle : 0.548 9.213 13839 Z= 0.277 Chirality : 0.040 0.140 1601 Planarity : 0.003 0.028 1715 Dihedral : 5.896 67.484 1412 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.84 % Allowed : 14.38 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1242 helix: 1.33 (0.19), residues: 762 sheet: -1.28 (0.55), residues: 78 loop : -1.75 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 912 HIS 0.004 0.001 HIS A 903 PHE 0.015 0.002 PHE A 941 TYR 0.012 0.001 TYR A 155 ARG 0.004 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.05768 ( 570) hydrogen bonds : angle 3.72027 ( 1683) covalent geometry : bond 0.00360 (10199) covalent geometry : angle 0.54797 (13839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 19 CYS cc_start: 0.8551 (m) cc_final: 0.7853 (p) REVERT: A 109 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8101 (tt0) REVERT: A 297 ASN cc_start: 0.8077 (m-40) cc_final: 0.7588 (t0) REVERT: A 840 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 842 ASP cc_start: 0.8814 (t0) cc_final: 0.8412 (t0) REVERT: A 1048 PHE cc_start: 0.8760 (t80) cc_final: 0.8449 (t80) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 0.2164 time to fit residues: 42.2460 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099277 restraints weight = 17008.134| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.05 r_work: 0.3167 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10199 Z= 0.128 Angle : 0.505 9.056 13839 Z= 0.255 Chirality : 0.039 0.139 1601 Planarity : 0.003 0.027 1715 Dihedral : 5.753 59.133 1412 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 16.96 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1242 helix: 1.56 (0.20), residues: 764 sheet: -0.98 (0.56), residues: 78 loop : -1.57 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 912 HIS 0.020 0.001 HIS A1111 PHE 0.009 0.001 PHE A 325 TYR 0.011 0.001 TYR A 358 ARG 0.002 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 570) hydrogen bonds : angle 3.62886 ( 1683) covalent geometry : bond 0.00280 (10199) covalent geometry : angle 0.50505 (13839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8445 (mmtm) REVERT: A 109 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8152 (tt0) REVERT: A 221 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 231 MET cc_start: 0.8460 (ttt) cc_final: 0.8225 (ttm) REVERT: A 297 ASN cc_start: 0.8062 (m-40) cc_final: 0.7607 (t0) REVERT: A 468 LEU cc_start: 0.8940 (pt) cc_final: 0.8704 (pp) REVERT: A 840 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: A 842 ASP cc_start: 0.8753 (t0) cc_final: 0.8369 (t0) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.2089 time to fit residues: 36.9338 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 22 optimal weight: 0.3980 overall best weight: 1.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097594 restraints weight = 17046.132| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.92 r_work: 0.3104 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10199 Z= 0.163 Angle : 0.548 9.628 13839 Z= 0.279 Chirality : 0.040 0.169 1601 Planarity : 0.003 0.033 1715 Dihedral : 5.657 55.349 1412 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 17.33 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1242 helix: 1.42 (0.19), residues: 781 sheet: -0.85 (0.55), residues: 80 loop : -1.64 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 912 HIS 0.003 0.001 HIS A1111 PHE 0.013 0.001 PHE A 941 TYR 0.017 0.001 TYR A 768 ARG 0.004 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.06154 ( 570) hydrogen bonds : angle 3.80920 ( 1683) covalent geometry : bond 0.00374 (10199) covalent geometry : angle 0.54753 (13839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8276 (tt0) REVERT: A 231 MET cc_start: 0.8571 (ttt) cc_final: 0.8343 (ttm) REVERT: A 246 ILE cc_start: 0.8488 (tt) cc_final: 0.8221 (tt) REVERT: A 297 ASN cc_start: 0.8087 (m-40) cc_final: 0.7497 (t0) REVERT: A 840 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: A 842 ASP cc_start: 0.8663 (t0) cc_final: 0.8328 (t0) REVERT: A 880 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7751 (ttp80) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.2169 time to fit residues: 39.3445 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097135 restraints weight = 17044.631| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.00 r_work: 0.3133 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10199 Z= 0.113 Angle : 0.496 9.464 13839 Z= 0.253 Chirality : 0.038 0.137 1601 Planarity : 0.003 0.031 1715 Dihedral : 5.452 60.095 1412 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.12 % Allowed : 18.53 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1242 helix: 1.67 (0.20), residues: 780 sheet: -0.59 (0.56), residues: 80 loop : -1.47 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 734 HIS 0.002 0.000 HIS A 213 PHE 0.009 0.001 PHE A 325 TYR 0.011 0.001 TYR A 768 ARG 0.006 0.000 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 570) hydrogen bonds : angle 3.62133 ( 1683) covalent geometry : bond 0.00231 (10199) covalent geometry : angle 0.49606 (13839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8330 (tt0) REVERT: A 231 MET cc_start: 0.8513 (ttt) cc_final: 0.8277 (ttm) REVERT: A 246 ILE cc_start: 0.8415 (tt) cc_final: 0.8155 (tt) REVERT: A 297 ASN cc_start: 0.8134 (m-40) cc_final: 0.7599 (t0) REVERT: A 840 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 842 ASP cc_start: 0.8569 (t0) cc_final: 0.8251 (t0) REVERT: A 1146 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (mp) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.2149 time to fit residues: 37.6542 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 80 optimal weight: 0.0020 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 chunk 4 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101683 restraints weight = 17098.953| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.00 r_work: 0.3201 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10199 Z= 0.100 Angle : 0.485 10.185 13839 Z= 0.244 Chirality : 0.038 0.142 1601 Planarity : 0.003 0.030 1715 Dihedral : 5.200 66.203 1412 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.03 % Allowed : 18.71 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1242 helix: 1.94 (0.20), residues: 775 sheet: -0.38 (0.57), residues: 80 loop : -1.34 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.001 0.000 HIS A 213 PHE 0.007 0.001 PHE A 418 TYR 0.012 0.001 TYR A 504 ARG 0.007 0.000 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 570) hydrogen bonds : angle 3.41633 ( 1683) covalent geometry : bond 0.00191 (10199) covalent geometry : angle 0.48537 (13839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8281 (tt0) REVERT: A 231 MET cc_start: 0.8417 (ttt) cc_final: 0.8171 (ttm) REVERT: A 246 ILE cc_start: 0.8410 (tt) cc_final: 0.8166 (tt) REVERT: A 297 ASN cc_start: 0.8013 (m-40) cc_final: 0.7533 (t0) REVERT: A 421 LYS cc_start: 0.7911 (tptp) cc_final: 0.7425 (mmtp) REVERT: A 840 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: A 842 ASP cc_start: 0.8477 (t0) cc_final: 0.8181 (t0) REVERT: A 899 PRO cc_start: 0.8278 (Cg_exo) cc_final: 0.8051 (Cg_endo) REVERT: A 1146 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7788 (mp) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 0.2596 time to fit residues: 46.9651 Evaluate side-chains 112 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096050 restraints weight = 17193.715| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.01 r_work: 0.3115 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10199 Z= 0.138 Angle : 0.525 10.054 13839 Z= 0.266 Chirality : 0.040 0.141 1601 Planarity : 0.003 0.030 1715 Dihedral : 5.404 70.929 1412 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.21 % Allowed : 18.71 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1242 helix: 1.87 (0.20), residues: 775 sheet: -0.39 (0.57), residues: 80 loop : -1.32 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1025 HIS 0.007 0.001 HIS A1111 PHE 0.011 0.001 PHE A 941 TYR 0.011 0.001 TYR A 504 ARG 0.006 0.000 ARG A1114 Details of bonding type rmsd hydrogen bonds : bond 0.05314 ( 570) hydrogen bonds : angle 3.59877 ( 1683) covalent geometry : bond 0.00315 (10199) covalent geometry : angle 0.52532 (13839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8342 (tt0) REVERT: A 170 MET cc_start: 0.9547 (tpp) cc_final: 0.9270 (mmt) REVERT: A 231 MET cc_start: 0.8569 (ttt) cc_final: 0.8350 (ttm) REVERT: A 246 ILE cc_start: 0.8491 (tt) cc_final: 0.8239 (tt) REVERT: A 297 ASN cc_start: 0.8113 (m-40) cc_final: 0.7586 (t0) REVERT: A 421 LYS cc_start: 0.8019 (tptp) cc_final: 0.7407 (mmtp) REVERT: A 840 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: A 842 ASP cc_start: 0.8558 (t0) cc_final: 0.8256 (t0) REVERT: A 1146 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7907 (mp) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 0.1956 time to fit residues: 32.9618 Evaluate side-chains 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098016 restraints weight = 17091.500| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.01 r_work: 0.3147 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10199 Z= 0.111 Angle : 0.508 9.879 13839 Z= 0.255 Chirality : 0.038 0.145 1601 Planarity : 0.003 0.033 1715 Dihedral : 5.388 72.207 1412 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.84 % Allowed : 18.80 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1242 helix: 1.93 (0.20), residues: 776 sheet: -0.31 (0.58), residues: 80 loop : -1.30 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 216 HIS 0.006 0.000 HIS A1111 PHE 0.008 0.001 PHE A 325 TYR 0.011 0.001 TYR A 504 ARG 0.006 0.000 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 570) hydrogen bonds : angle 3.52017 ( 1683) covalent geometry : bond 0.00228 (10199) covalent geometry : angle 0.50813 (13839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8358 (tt0) REVERT: A 246 ILE cc_start: 0.8437 (tt) cc_final: 0.8191 (tt) REVERT: A 297 ASN cc_start: 0.8046 (m-40) cc_final: 0.7551 (t0) REVERT: A 421 LYS cc_start: 0.7983 (tptp) cc_final: 0.7415 (mmtp) REVERT: A 840 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 1146 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7814 (mp) outliers start: 20 outliers final: 16 residues processed: 114 average time/residue: 0.2062 time to fit residues: 34.7903 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 4.9990 chunk 110 optimal weight: 0.0040 chunk 71 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097549 restraints weight = 17233.412| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.01 r_work: 0.3134 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10199 Z= 0.118 Angle : 0.513 9.735 13839 Z= 0.259 Chirality : 0.039 0.147 1601 Planarity : 0.003 0.031 1715 Dihedral : 5.455 75.934 1412 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.84 % Allowed : 18.99 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1242 helix: 1.93 (0.20), residues: 776 sheet: -0.32 (0.57), residues: 80 loop : -1.30 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1025 HIS 0.002 0.000 HIS A 213 PHE 0.009 0.001 PHE A 325 TYR 0.017 0.001 TYR A 504 ARG 0.002 0.000 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 570) hydrogen bonds : angle 3.54577 ( 1683) covalent geometry : bond 0.00255 (10199) covalent geometry : angle 0.51252 (13839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8356 (tt0) REVERT: A 246 ILE cc_start: 0.8436 (tt) cc_final: 0.8190 (tt) REVERT: A 297 ASN cc_start: 0.8063 (m-40) cc_final: 0.7572 (t0) REVERT: A 421 LYS cc_start: 0.8058 (tptp) cc_final: 0.7508 (mmtp) REVERT: A 840 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: A 1146 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7833 (mp) outliers start: 20 outliers final: 18 residues processed: 115 average time/residue: 0.2036 time to fit residues: 34.7144 Evaluate side-chains 113 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 840 PHE Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 94 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099430 restraints weight = 16946.294| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.89 r_work: 0.3122 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10199 Z= 0.133 Angle : 0.526 9.382 13839 Z= 0.266 Chirality : 0.039 0.146 1601 Planarity : 0.003 0.030 1715 Dihedral : 5.573 79.605 1412 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.94 % Allowed : 18.99 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1242 helix: 1.95 (0.20), residues: 769 sheet: -0.35 (0.57), residues: 80 loop : -1.26 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1025 HIS 0.002 0.000 HIS A 934 PHE 0.010 0.001 PHE A 941 TYR 0.015 0.001 TYR A 504 ARG 0.002 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.05344 ( 570) hydrogen bonds : angle 3.61122 ( 1683) covalent geometry : bond 0.00298 (10199) covalent geometry : angle 0.52621 (13839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4786.42 seconds wall clock time: 85 minutes 11.20 seconds (5111.20 seconds total)