Starting phenix.real_space_refine on Wed Sep 25 09:02:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_35837.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_35837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_35837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_35837.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iza_35837/09_2024/8iza_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-5461/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: 6.05, per 1000 atoms: 0.61 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: 2.52 Conformation dependent library (CDL) restraints added in 1.0 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: 1.20 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: 3.72 Time building geometry restraints manager: 2.95 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.720 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: 0.010 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: 31.330 ------------------------------------------------------------------------------- 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= 0.195 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.095 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: 0.2421 time to fit residues: 73.5991 Evaluate side-chains 130 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10199 Z= 0.222 Angle : 0.553 7.834 13839 Z= 0.284 Chirality : 0.040 0.168 1601 Planarity : 0.003 0.029 1715 Dihedral : 5.864 78.227 1412 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.45 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7839 (tt0) REVERT: A 297 ASN cc_start: 0.7921 (m-40) cc_final: 0.7429 (t0) REVERT: A 468 LEU cc_start: 0.8273 (pt) cc_final: 0.8013 (pp) REVERT: A 744 MET cc_start: 0.6061 (tmm) cc_final: 0.5808 (tmm) REVERT: A 828 ASP cc_start: 0.8550 (m-30) cc_final: 0.7931 (m-30) REVERT: A 842 ASP cc_start: 0.8465 (t0) cc_final: 0.7885 (t0) REVERT: A 1272 MET cc_start: 0.8886 (ptp) cc_final: 0.8605 (ptm) outliers start: 22 outliers final: 14 residues processed: 160 average time/residue: 0.2051 time to fit residues: 47.4810 Evaluate side-chains 124 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A1111 HIS ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3569 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= 0.133 Angle : 0.463 10.178 13839 Z= 0.232 Chirality : 0.038 0.134 1601 Planarity : 0.003 0.029 1715 Dihedral : 5.440 84.349 1412 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.57 % Allowed : 13.82 % Favored : 84.61 % 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: 0.42 (0.24), residues: 1242 helix: 1.46 (0.20), residues: 766 sheet: -1.01 (0.59), residues: 71 loop : -1.83 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 912 HIS 0.003 0.000 HIS A 213 PHE 0.023 0.001 PHE A 993 TYR 0.007 0.001 TYR A 881 ARG 0.003 0.000 ARG A 274 *********************** 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 fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7930 (tt0) REVERT: A 297 ASN cc_start: 0.7769 (m-40) cc_final: 0.7325 (t0) REVERT: A 319 MET cc_start: 0.8551 (tpp) cc_final: 0.8274 (tpp) REVERT: A 468 LEU cc_start: 0.8364 (pt) cc_final: 0.8141 (pp) REVERT: A 842 ASP cc_start: 0.8451 (t0) cc_final: 0.7927 (t0) REVERT: A 1272 MET cc_start: 0.8730 (ptp) cc_final: 0.8463 (ptm) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.1996 time to fit residues: 39.2894 Evaluate side-chains 124 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 336 PHE 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 985 TYR Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1084 LEU 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 111 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 849 GLN ** A1154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10199 Z= 0.412 Angle : 0.682 9.914 13839 Z= 0.353 Chirality : 0.044 0.155 1601 Planarity : 0.004 0.036 1715 Dihedral : 6.503 73.741 1412 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.40 % Allowed : 16.22 % Favored : 81.38 % 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: -0.14 (0.24), residues: 1242 helix: 0.92 (0.19), residues: 782 sheet: -1.36 (0.54), residues: 78 loop : -1.90 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1025 HIS 0.017 0.001 HIS A1111 PHE 0.021 0.002 PHE A 698 TYR 0.023 0.002 TYR A 289 ARG 0.006 0.001 ARG A 272 *********************** 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 133 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8330 (tt0) REVERT: A 186 MET cc_start: 0.9237 (mmt) cc_final: 0.8981 (tpt) REVERT: A 231 MET cc_start: 0.8329 (ttt) cc_final: 0.8107 (ttm) REVERT: A 297 ASN cc_start: 0.8093 (m-40) cc_final: 0.7648 (t0) REVERT: A 840 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: A 842 ASP cc_start: 0.8290 (t0) cc_final: 0.8030 (t0) REVERT: A 1168 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8135 (p) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.2325 time to fit residues: 41.5978 Evaluate side-chains 106 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 107 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 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 1010 VAL Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1165 LYS Chi-restraints excluded: chain A residue 1168 THR 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 99 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 994 GLN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10199 Z= 0.161 Angle : 0.495 7.083 13839 Z= 0.258 Chirality : 0.039 0.139 1601 Planarity : 0.003 0.029 1715 Dihedral : 5.915 58.828 1412 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 18.16 % Favored : 80.18 % 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: 0.45 (0.24), residues: 1242 helix: 1.38 (0.19), residues: 774 sheet: -1.04 (0.55), residues: 78 loop : -1.62 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 734 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE A 698 TYR 0.011 0.001 TYR A 768 ARG 0.003 0.000 ARG A 274 *********************** 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 116 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9182 (mmt) cc_final: 0.8943 (tpt) REVERT: A 231 MET cc_start: 0.8240 (ttt) cc_final: 0.8001 (ttm) REVERT: A 246 ILE cc_start: 0.8585 (tt) cc_final: 0.8299 (tt) REVERT: A 297 ASN cc_start: 0.7991 (m-40) cc_final: 0.7545 (t0) REVERT: A 840 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: A 842 ASP cc_start: 0.8210 (t0) cc_final: 0.7937 (t0) REVERT: A 1168 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8120 (p) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.2382 time to fit residues: 40.1481 Evaluate side-chains 103 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 856 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 1168 THR 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 40 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10199 Z= 0.279 Angle : 0.569 9.607 13839 Z= 0.297 Chirality : 0.041 0.173 1601 Planarity : 0.004 0.030 1715 Dihedral : 5.822 61.439 1412 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.67 % Allowed : 18.16 % 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: 0.33 (0.24), residues: 1242 helix: 1.25 (0.19), residues: 787 sheet: -1.09 (0.54), residues: 78 loop : -1.68 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1025 HIS 0.005 0.001 HIS A 153 PHE 0.018 0.001 PHE A 698 TYR 0.016 0.001 TYR A 504 ARG 0.005 0.000 ARG A 272 *********************** 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 123 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.8116 (tp) cc_final: 0.7620 (tt) REVERT: A 186 MET cc_start: 0.9191 (mmt) cc_final: 0.8899 (tpt) REVERT: A 231 MET cc_start: 0.8377 (ttt) cc_final: 0.8161 (ttm) REVERT: A 246 ILE cc_start: 0.8544 (tt) cc_final: 0.8264 (tt) REVERT: A 297 ASN cc_start: 0.8120 (m-40) cc_final: 0.7633 (t0) REVERT: A 840 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: A 842 ASP cc_start: 0.8225 (t0) cc_final: 0.7999 (t0) REVERT: A 1168 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8336 (p) outliers start: 29 outliers final: 21 residues processed: 115 average time/residue: 0.1867 time to fit residues: 32.5772 Evaluate side-chains 113 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 363 LEU 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 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 866 ILE Chi-restraints excluded: chain A residue 985 TYR Chi-restraints excluded: chain A residue 1006 MET 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 1168 THR 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 115 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10199 Z= 0.162 Angle : 0.499 7.967 13839 Z= 0.259 Chirality : 0.039 0.150 1601 Planarity : 0.003 0.031 1715 Dihedral : 5.578 68.814 1412 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.03 % Allowed : 19.63 % Favored : 78.34 % 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: 0.77 (0.25), residues: 1242 helix: 1.60 (0.19), residues: 777 sheet: -0.76 (0.55), residues: 80 loop : -1.47 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 734 HIS 0.005 0.000 HIS A 153 PHE 0.013 0.001 PHE A 698 TYR 0.011 0.001 TYR A 504 ARG 0.002 0.000 ARG A 503 *********************** 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 116 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7983 (tp) cc_final: 0.7476 (tt) REVERT: A 186 MET cc_start: 0.9127 (mmt) cc_final: 0.8899 (tpt) REVERT: A 231 MET cc_start: 0.8266 (ttt) cc_final: 0.8033 (ttm) REVERT: A 246 ILE cc_start: 0.8460 (tt) cc_final: 0.8187 (tt) REVERT: A 297 ASN cc_start: 0.8071 (m-40) cc_final: 0.7651 (t0) REVERT: A 744 MET cc_start: 0.6826 (tmm) cc_final: 0.6549 (tmm) REVERT: A 840 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 842 ASP cc_start: 0.8086 (t0) cc_final: 0.7877 (t0) REVERT: A 1168 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8342 (p) outliers start: 22 outliers final: 17 residues processed: 111 average time/residue: 0.2030 time to fit residues: 33.3308 Evaluate side-chains 108 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR 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 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 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1168 THR 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 73 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10199 Z= 0.192 Angle : 0.508 7.875 13839 Z= 0.263 Chirality : 0.039 0.142 1601 Planarity : 0.003 0.030 1715 Dihedral : 5.621 77.374 1412 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.94 % Allowed : 19.82 % Favored : 78.25 % 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: 0.81 (0.25), residues: 1242 helix: 1.59 (0.19), residues: 783 sheet: -0.72 (0.55), residues: 80 loop : -1.45 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1025 HIS 0.005 0.001 HIS A 153 PHE 0.014 0.001 PHE A 698 TYR 0.012 0.001 TYR A 504 ARG 0.006 0.000 ARG A 531 *********************** 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 115 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.8021 (tp) cc_final: 0.7509 (tt) REVERT: A 170 MET cc_start: 0.9293 (mmt) cc_final: 0.8751 (tpt) REVERT: A 186 MET cc_start: 0.9127 (mmt) cc_final: 0.8894 (tpt) REVERT: A 246 ILE cc_start: 0.8457 (tt) cc_final: 0.8197 (tt) REVERT: A 297 ASN cc_start: 0.8070 (m-40) cc_final: 0.7641 (t0) REVERT: A 744 MET cc_start: 0.6879 (tmm) cc_final: 0.6623 (tmm) REVERT: A 840 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 1168 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8387 (p) outliers start: 21 outliers final: 19 residues processed: 113 average time/residue: 0.1881 time to fit residues: 32.1531 Evaluate side-chains 109 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR 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 377 SER 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 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1168 THR 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 114 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 0.0020 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10199 Z= 0.157 Angle : 0.495 7.415 13839 Z= 0.257 Chirality : 0.039 0.145 1601 Planarity : 0.003 0.036 1715 Dihedral : 5.555 77.893 1412 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.21 % Allowed : 19.35 % Favored : 78.43 % 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: 0.97 (0.25), residues: 1242 helix: 1.72 (0.20), residues: 783 sheet: -0.59 (0.56), residues: 80 loop : -1.39 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.005 0.000 HIS A 153 PHE 0.012 0.001 PHE A 698 TYR 0.010 0.001 TYR A 504 ARG 0.006 0.000 ARG A 531 *********************** 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 121 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.080 Fit side-chains REVERT: A 93 LEU cc_start: 0.8030 (tp) cc_final: 0.7516 (tt) REVERT: A 170 MET cc_start: 0.9280 (mmt) cc_final: 0.8853 (tpt) REVERT: A 186 MET cc_start: 0.9099 (mmt) cc_final: 0.8863 (tpt) REVERT: A 246 ILE cc_start: 0.8447 (tt) cc_final: 0.8195 (tt) REVERT: A 297 ASN cc_start: 0.8006 (m-40) cc_final: 0.7591 (t0) REVERT: A 744 MET cc_start: 0.6950 (tmm) cc_final: 0.6725 (tmm) REVERT: A 840 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: A 1168 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8435 (p) outliers start: 24 outliers final: 17 residues processed: 115 average time/residue: 0.1887 time to fit residues: 32.8165 Evaluate side-chains 109 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 377 SER 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 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE 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 1168 THR 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 117 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10199 Z= 0.174 Angle : 0.505 7.221 13839 Z= 0.262 Chirality : 0.039 0.146 1601 Planarity : 0.003 0.031 1715 Dihedral : 5.578 80.278 1412 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.75 % Allowed : 19.82 % Favored : 78.43 % 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: 0.97 (0.25), residues: 1242 helix: 1.70 (0.20), residues: 781 sheet: -0.51 (0.56), residues: 80 loop : -1.34 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.005 0.000 HIS A 153 PHE 0.013 0.001 PHE A 698 TYR 0.010 0.001 TYR A 504 ARG 0.002 0.000 ARG A 274 ********************** 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 113 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.8036 (tp) cc_final: 0.7516 (tt) REVERT: A 186 MET cc_start: 0.9114 (mmt) cc_final: 0.8867 (tpt) REVERT: A 246 ILE cc_start: 0.8454 (tt) cc_final: 0.8204 (tt) REVERT: A 297 ASN cc_start: 0.8020 (m-40) cc_final: 0.7608 (t0) REVERT: A 744 MET cc_start: 0.6961 (tmm) cc_final: 0.6728 (tmm) REVERT: A 840 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 842 ASP cc_start: 0.8270 (t0) cc_final: 0.7905 (t0) REVERT: A 1168 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8440 (p) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.1988 time to fit residues: 33.2678 Evaluate side-chains 110 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 377 SER 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 856 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1168 THR 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 104 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099424 restraints weight = 16884.062| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.91 r_work: 0.3118 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10199 Z= 0.163 Angle : 0.502 7.116 13839 Z= 0.259 Chirality : 0.039 0.145 1601 Planarity : 0.003 0.031 1715 Dihedral : 5.569 81.554 1412 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.75 % Allowed : 19.72 % Favored : 78.53 % 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: 1.03 (0.25), residues: 1242 helix: 1.74 (0.20), residues: 781 sheet: -0.44 (0.56), residues: 80 loop : -1.31 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 HIS 0.005 0.000 HIS A 153 PHE 0.013 0.001 PHE A 698 TYR 0.010 0.001 TYR A 504 ARG 0.002 0.000 ARG A 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.91 seconds wall clock time: 40 minutes 0.76 seconds (2400.76 seconds total)