Starting phenix.real_space_refine on Thu May 15 05:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.map" model { file = "/net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dus_47176/05_2025/9dus_47176.cif" } resolution = 3.12 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= 0.017 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8101 2.51 5 N 2201 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12702 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10069 Classifications: {'peptide': 1253} Link IDs: {'PTRANS': 52, 'TRANS': 1200} Chain breaks: 6 Chain: "B" Number of atoms: 576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 570 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 74, 570 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 bond proxies already assigned to first conformer: 567 Chain: "C" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1039 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 1 Chain: "D" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "E" Number of atoms: 576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Conformer: "B" Number of residues, atoms: 74, 571 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} bond proxies already assigned to first conformer: 571 Time building chain proxies: 8.69, per 1000 atoms: 0.68 Number of scatterers: 12702 At special positions: 0 Unit cell: (99.1573, 107.125, 165.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2338 8.00 N 2201 7.00 C 8101 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 61.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 4.009A pdb=" N ILE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 4.440A pdb=" N LYS A 50 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.758A pdb=" N GLU A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 103 through 135 removed outlier: 3.584A pdb=" N ARG A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYS A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 removed outlier: 4.041A pdb=" N GLU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.696A pdb=" N PHE A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.734A pdb=" N GLY A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 275 through 293 removed outlier: 4.034A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 4.336A pdb=" N LEU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 removed outlier: 3.787A pdb=" N ASN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.824A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.745A pdb=" N ILE A 349 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.020A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.529A pdb=" N PHE A 443 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 4.244A pdb=" N VAL A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.523A pdb=" N LEU A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.622A pdb=" N VAL A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.904A pdb=" N VAL A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.680A pdb=" N PHE A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 573' Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.682A pdb=" N ASN A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.827A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.664A pdb=" N LYS A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 743 through 763 Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.698A pdb=" N LYS A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 793 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 814 " --> pdb=" O ARG A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.376A pdb=" N ILE A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 removed outlier: 3.642A pdb=" N ALA A 867 " --> pdb=" O GLU A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 913 through 923 removed outlier: 3.608A pdb=" N ILE A 918 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Proline residue: A 919 - end of helix Processing helix chain 'A' and resid 923 through 933 removed outlier: 3.654A pdb=" N LEU A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 955 through 970 Processing helix chain 'A' and resid 975 through 983 removed outlier: 3.897A pdb=" N HIS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.059A pdb=" N LYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1050 removed outlier: 3.640A pdb=" N GLU A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.734A pdb=" N ALA A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1079 removed outlier: 3.695A pdb=" N LEU A1079 " --> pdb=" O ILE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1093 removed outlier: 3.884A pdb=" N ILE A1086 " --> pdb=" O THR A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1104 Processing helix chain 'A' and resid 1105 through 1120 Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1161 through 1165 Processing helix chain 'A' and resid 1176 through 1183 removed outlier: 3.649A pdb=" N CYS A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1252 through 1264 removed outlier: 3.749A pdb=" N ASN A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A1258 " --> pdb=" O SER A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1304 through 1309 Processing helix chain 'A' and resid 1330 through 1348 Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.558A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 368 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'C' and resid 324 through 371 removed outlier: 3.992A pdb=" N GLY C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 removed outlier: 4.087A pdb=" N ARG C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 488 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'D' and resid 325 through 369 removed outlier: 3.834A pdb=" N GLY D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 removed outlier: 4.260A pdb=" N SER E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 374 removed outlier: 4.040A pdb=" N GLU E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.574A pdb=" N ASP E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.384A pdb=" N SER A 83 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR A 222 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 219 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381 removed outlier: 6.888A pdb=" N ILE B 398 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.559A pdb=" N LYS A 447 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.958A pdb=" N TYR A 706 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 770 removed outlier: 3.544A pdb=" N VAL A 656 " --> pdb=" O LYS A 781 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AA7, first strand: chain 'A' and resid 1166 through 1171 removed outlier: 3.657A pdb=" N VAL A1360 " --> pdb=" O ILE A1171 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2053 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: 3.86 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4094 1.34 - 1.46: 2065 1.46 - 1.58: 6687 1.58 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 12949 Sorted by residual: bond pdb=" C PHE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.335 1.363 -0.027 1.36e-02 5.41e+03 4.04e+00 bond pdb=" N ILE A 752 " pdb=" CA ILE A 752 " ideal model delta sigma weight residual 1.464 1.486 -0.022 1.23e-02 6.61e+03 3.18e+00 bond pdb=" C ILE A 918 " pdb=" N PRO A 919 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.02e+00 bond pdb=" C ILE A 752 " pdb=" N PRO A 753 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.01e+00 bond pdb=" CA ILE A 752 " pdb=" C ILE A 752 " ideal model delta sigma weight residual 1.520 1.534 -0.014 8.80e-03 1.29e+04 2.70e+00 ... (remaining 12944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 17062 1.98 - 3.97: 369 3.97 - 5.95: 47 5.95 - 7.93: 20 7.93 - 9.91: 3 Bond angle restraints: 17501 Sorted by residual: angle pdb=" C THR A1082 " pdb=" CA THR A1082 " pdb=" CB THR A1082 " ideal model delta sigma weight residual 115.79 110.22 5.57 1.19e+00 7.06e-01 2.19e+01 angle pdb=" C LEU E 394 " pdb=" N LYS E 395 " pdb=" CA LYS E 395 " ideal model delta sigma weight residual 121.80 131.40 -9.60 2.44e+00 1.68e-01 1.55e+01 angle pdb=" C ALA C 373 " pdb=" N ILE C 374 " pdb=" CA ILE C 374 " ideal model delta sigma weight residual 122.13 128.79 -6.66 1.85e+00 2.92e-01 1.29e+01 angle pdb=" C GLY A 741 " pdb=" N TYR A 742 " pdb=" CA TYR A 742 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C PRO E 392 " pdb=" N ASP E 393 " pdb=" CA ASP E 393 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 ... (remaining 17496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 7240 14.99 - 29.97: 525 29.97 - 44.96: 119 44.96 - 59.95: 9 59.95 - 74.94: 7 Dihedral angle restraints: 7900 sinusoidal: 3248 harmonic: 4652 Sorted by residual: dihedral pdb=" CA ILE E 390 " pdb=" C ILE E 390 " pdb=" N ASN E 391 " pdb=" CA ASN E 391 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA HIS A1174 " pdb=" C HIS A1174 " pdb=" N GLU A1175 " pdb=" CA GLU A1175 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ILE A 766 " pdb=" C ILE A 766 " pdb=" N ALA A 767 " pdb=" CA ALA A 767 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1880 0.095 - 0.190: 114 0.190 - 0.286: 5 0.286 - 0.381: 0 0.381 - 0.476: 1 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CG LEU A 705 " pdb=" CB LEU A 705 " pdb=" CD1 LEU A 705 " pdb=" CD2 LEU A 705 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CB ILE E 372 " pdb=" CA ILE E 372 " pdb=" CG1 ILE E 372 " pdb=" CG2 ILE E 372 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP A 466 " pdb=" N ASP A 466 " pdb=" C ASP A 466 " pdb=" CB ASP A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 1997 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 274 " 0.055 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 275 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 408 " -0.016 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP A 408 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 408 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 408 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 408 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 408 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 408 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 408 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 408 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 408 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 752 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO A 753 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 753 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 753 " 0.041 5.00e-02 4.00e+02 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3580 2.83 - 3.34: 11524 3.34 - 3.86: 20296 3.86 - 4.38: 24016 4.38 - 4.90: 41638 Nonbonded interactions: 101054 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" OD1 ASP A 335 " model vdw 2.307 3.040 nonbonded pdb=" O TRP A 747 " pdb=" OG1 THR A 751 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR A 673 " pdb=" OE1 GLN A 694 " model vdw 2.355 3.040 nonbonded pdb=" O LEU A1274 " pdb=" OG1 THR A1278 " model vdw 2.361 3.040 nonbonded pdb=" O ALA A 796 " pdb=" OG1 THR A 800 " model vdw 2.365 3.040 ... (remaining 101049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 5.850 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.590 Find NCS groups from input model: 0.260 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.004 0.068 12949 Z= 0.186 Angle : 0.731 9.915 17501 Z= 0.402 Chirality : 0.048 0.476 2000 Planarity : 0.008 0.082 2212 Dihedral : 11.116 74.935 4888 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.18), residues: 1566 helix: -0.60 (0.14), residues: 873 sheet: 0.98 (0.59), residues: 80 loop : -1.43 (0.22), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 408 HIS 0.008 0.001 HIS A 812 PHE 0.029 0.002 PHE A 304 TYR 0.026 0.002 TYR A 522 ARG 0.004 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.18792 ( 708) hydrogen bonds : angle 6.45483 ( 2053) covalent geometry : bond 0.00369 (12949) covalent geometry : angle 0.73148 (17501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7115 (mtt180) REVERT: A 50 LYS cc_start: 0.8240 (ttmt) cc_final: 0.8002 (mtpp) REVERT: A 62 ILE cc_start: 0.7905 (mm) cc_final: 0.7471 (mt) REVERT: A 111 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7335 (ttmm) REVERT: A 355 SER cc_start: 0.8255 (m) cc_final: 0.7989 (p) REVERT: A 361 LEU cc_start: 0.8234 (mt) cc_final: 0.7991 (mt) REVERT: A 435 GLN cc_start: 0.8520 (mt0) cc_final: 0.8281 (mt0) REVERT: A 500 ASP cc_start: 0.6941 (t0) cc_final: 0.6491 (t70) REVERT: A 516 TYR cc_start: 0.8101 (t80) cc_final: 0.7788 (t80) REVERT: A 533 SER cc_start: 0.7921 (t) cc_final: 0.7495 (p) REVERT: A 535 LYS cc_start: 0.8135 (tppt) cc_final: 0.7927 (mmtp) REVERT: A 546 PHE cc_start: 0.7164 (p90) cc_final: 0.6677 (p90) REVERT: A 559 ILE cc_start: 0.8339 (mt) cc_final: 0.7932 (mt) REVERT: A 563 LEU cc_start: 0.7655 (mt) cc_final: 0.7399 (mp) REVERT: A 570 LYS cc_start: 0.8022 (mttt) cc_final: 0.7769 (mttt) REVERT: A 573 LYS cc_start: 0.7532 (mtpp) cc_final: 0.7324 (mtpp) REVERT: A 861 VAL cc_start: 0.7413 (t) cc_final: 0.7136 (m) REVERT: A 923 ASN cc_start: 0.8299 (t0) cc_final: 0.7986 (t0) REVERT: A 925 ASP cc_start: 0.7296 (m-30) cc_final: 0.7015 (m-30) REVERT: A 1019 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7337 (mtp85) REVERT: A 1090 MET cc_start: 0.7006 (ttt) cc_final: 0.6648 (ttt) REVERT: A 1144 MET cc_start: 0.8124 (mmm) cc_final: 0.7841 (mmm) REVERT: A 1240 ARG cc_start: 0.7386 (tpt170) cc_final: 0.7169 (mmm160) REVERT: A 1352 LYS cc_start: 0.7286 (mttt) cc_final: 0.7011 (mttt) REVERT: C 371 MET cc_start: 0.6812 (ptp) cc_final: 0.6579 (ptp) REVERT: C 460 SER cc_start: 0.7749 (p) cc_final: 0.7450 (m) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2776 time to fit residues: 116.5657 Evaluate side-chains 258 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 0.0030 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.0060 chunk 142 optimal weight: 0.5980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 HIS A 809 GLN B 329 ASN C 356 GLN E 329 ASN E 356 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121781 restraints weight = 36873.639| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.49 r_work: 0.3259 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12949 Z= 0.131 Angle : 0.514 7.363 17501 Z= 0.278 Chirality : 0.039 0.144 2000 Planarity : 0.005 0.050 2212 Dihedral : 4.308 23.955 1735 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.42 % Allowed : 6.27 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.20), residues: 1566 helix: 1.52 (0.17), residues: 887 sheet: 1.28 (0.55), residues: 97 loop : -1.16 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1189 HIS 0.011 0.001 HIS A 157 PHE 0.019 0.002 PHE A 392 TYR 0.019 0.001 TYR A 789 ARG 0.007 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.05866 ( 708) hydrogen bonds : angle 4.37992 ( 2053) covalent geometry : bond 0.00265 (12949) covalent geometry : angle 0.51420 (17501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 271 time to evaluate : 1.353 Fit side-chains REVERT: A 33 ARG cc_start: 0.7524 (mtt90) cc_final: 0.7271 (mtt-85) REVERT: A 50 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8122 (mtpp) REVERT: A 77 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7681 (ttm-80) REVERT: A 264 LEU cc_start: 0.8202 (tp) cc_final: 0.8000 (tp) REVERT: A 355 SER cc_start: 0.8466 (m) cc_final: 0.8231 (p) REVERT: A 361 LEU cc_start: 0.8291 (mt) cc_final: 0.8070 (mt) REVERT: A 500 ASP cc_start: 0.6948 (t0) cc_final: 0.6571 (t70) REVERT: A 516 TYR cc_start: 0.8093 (t80) cc_final: 0.7839 (t80) REVERT: A 535 LYS cc_start: 0.8180 (tppt) cc_final: 0.7923 (mmtp) REVERT: A 570 LYS cc_start: 0.8166 (mttt) cc_final: 0.7895 (mttt) REVERT: A 573 LYS cc_start: 0.7572 (mtpp) cc_final: 0.7354 (mtpp) REVERT: A 752 ILE cc_start: 0.8544 (mt) cc_final: 0.8278 (mp) REVERT: A 780 THR cc_start: 0.7943 (m) cc_final: 0.7662 (p) REVERT: A 803 TYR cc_start: 0.8185 (t80) cc_final: 0.7953 (t80) REVERT: A 861 VAL cc_start: 0.7489 (t) cc_final: 0.7186 (m) REVERT: A 923 ASN cc_start: 0.8364 (t0) cc_final: 0.7943 (t0) REVERT: A 925 ASP cc_start: 0.7322 (m-30) cc_final: 0.7066 (m-30) REVERT: A 930 MET cc_start: 0.7862 (ttp) cc_final: 0.7606 (ttp) REVERT: A 969 LEU cc_start: 0.8397 (tp) cc_final: 0.8174 (tt) REVERT: A 1062 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 1090 MET cc_start: 0.7095 (ttt) cc_final: 0.6760 (ttt) REVERT: A 1112 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7466 (ttm-80) REVERT: A 1144 MET cc_start: 0.8200 (mmm) cc_final: 0.7835 (mmm) REVERT: A 1150 ARG cc_start: 0.7530 (mtm110) cc_final: 0.7302 (mtp180) REVERT: A 1240 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7166 (mmm160) REVERT: A 1352 LYS cc_start: 0.7332 (mttt) cc_final: 0.7048 (mttt) REVERT: C 446 MET cc_start: 0.5998 (mmt) cc_final: 0.5776 (mmt) REVERT: C 460 SER cc_start: 0.7808 (p) cc_final: 0.7521 (m) outliers start: 6 outliers final: 5 residues processed: 272 average time/residue: 0.2836 time to fit residues: 107.3227 Evaluate side-chains 269 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain E residue 371 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 144 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 71 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN A 809 GLN A1186 ASN C 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118302 restraints weight = 34650.449| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.43 r_work: 0.3221 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12949 Z= 0.163 Angle : 0.525 6.826 17501 Z= 0.280 Chirality : 0.041 0.152 2000 Planarity : 0.004 0.040 2212 Dihedral : 4.269 23.424 1735 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.41 % Allowed : 6.90 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1566 helix: 1.95 (0.17), residues: 897 sheet: 1.06 (0.53), residues: 97 loop : -1.17 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 408 HIS 0.011 0.001 HIS A 157 PHE 0.020 0.002 PHE A 304 TYR 0.021 0.002 TYR A 516 ARG 0.004 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.05790 ( 708) hydrogen bonds : angle 4.26937 ( 2053) covalent geometry : bond 0.00370 (12949) covalent geometry : angle 0.52473 (17501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 273 time to evaluate : 1.402 Fit side-chains REVERT: A 33 ARG cc_start: 0.7540 (mtt90) cc_final: 0.7240 (mtt-85) REVERT: A 50 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8223 (mtpp) REVERT: A 264 LEU cc_start: 0.8240 (tp) cc_final: 0.8024 (tp) REVERT: A 355 SER cc_start: 0.8432 (m) cc_final: 0.8199 (p) REVERT: A 361 LEU cc_start: 0.8301 (mt) cc_final: 0.8083 (mt) REVERT: A 435 GLN cc_start: 0.8434 (mt0) cc_final: 0.8201 (mt0) REVERT: A 504 ASN cc_start: 0.6868 (m-40) cc_final: 0.6313 (t0) REVERT: A 535 LYS cc_start: 0.8167 (tppt) cc_final: 0.7966 (mmtp) REVERT: A 570 LYS cc_start: 0.8152 (mttt) cc_final: 0.7882 (mttt) REVERT: A 573 LYS cc_start: 0.7474 (mtpp) cc_final: 0.7232 (mtpp) REVERT: A 780 THR cc_start: 0.7947 (m) cc_final: 0.7670 (p) REVERT: A 803 TYR cc_start: 0.8240 (t80) cc_final: 0.7886 (t80) REVERT: A 861 VAL cc_start: 0.7631 (t) cc_final: 0.7324 (m) REVERT: A 923 ASN cc_start: 0.8336 (t0) cc_final: 0.7918 (t0) REVERT: A 925 ASP cc_start: 0.7348 (m-30) cc_final: 0.7095 (m-30) REVERT: A 930 MET cc_start: 0.7889 (ttp) cc_final: 0.7664 (ttp) REVERT: A 1090 MET cc_start: 0.7042 (ttt) cc_final: 0.6744 (ttt) REVERT: A 1108 TYR cc_start: 0.7866 (t80) cc_final: 0.7499 (t80) REVERT: A 1110 GLN cc_start: 0.7274 (mt0) cc_final: 0.6973 (mt0) REVERT: A 1112 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7438 (ttm-80) REVERT: A 1150 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7253 (mtp180) REVERT: A 1240 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7163 (mmm160) REVERT: A 1352 LYS cc_start: 0.7461 (mttt) cc_final: 0.7188 (mttt) REVERT: C 460 SER cc_start: 0.7812 (p) cc_final: 0.7550 (m) outliers start: 20 outliers final: 16 residues processed: 278 average time/residue: 0.2949 time to fit residues: 113.2866 Evaluate side-chains 279 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1132 CYS Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 66 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 123 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 117 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 809 GLN A1186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118095 restraints weight = 41360.362| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.88 r_work: 0.3219 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12949 Z= 0.125 Angle : 0.490 7.023 17501 Z= 0.260 Chirality : 0.039 0.151 2000 Planarity : 0.004 0.042 2212 Dihedral : 4.118 22.943 1735 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.48 % Allowed : 8.87 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.21), residues: 1566 helix: 2.30 (0.17), residues: 892 sheet: 0.95 (0.53), residues: 97 loop : -1.13 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1189 HIS 0.011 0.001 HIS A 157 PHE 0.023 0.002 PHE A 546 TYR 0.016 0.001 TYR A 516 ARG 0.005 0.000 ARG A 782 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 708) hydrogen bonds : angle 4.11479 ( 2053) covalent geometry : bond 0.00268 (12949) covalent geometry : angle 0.49010 (17501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 1.584 Fit side-chains REVERT: A 33 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7222 (mtt-85) REVERT: A 50 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8317 (mtpp) REVERT: A 355 SER cc_start: 0.8448 (m) cc_final: 0.8158 (p) REVERT: A 435 GLN cc_start: 0.8444 (mt0) cc_final: 0.8171 (mt0) REVERT: A 504 ASN cc_start: 0.6969 (m-40) cc_final: 0.6309 (t0) REVERT: A 522 TYR cc_start: 0.8248 (p90) cc_final: 0.7776 (p90) REVERT: A 535 LYS cc_start: 0.8178 (tppt) cc_final: 0.7919 (mmtp) REVERT: A 570 LYS cc_start: 0.8174 (mttt) cc_final: 0.7878 (mttt) REVERT: A 573 LYS cc_start: 0.7443 (mtpp) cc_final: 0.7190 (mtpp) REVERT: A 752 ILE cc_start: 0.8495 (mt) cc_final: 0.8251 (mp) REVERT: A 780 THR cc_start: 0.7984 (m) cc_final: 0.7708 (p) REVERT: A 803 TYR cc_start: 0.8248 (t80) cc_final: 0.7841 (t80) REVERT: A 861 VAL cc_start: 0.7584 (t) cc_final: 0.7295 (m) REVERT: A 923 ASN cc_start: 0.8309 (t0) cc_final: 0.7839 (t0) REVERT: A 925 ASP cc_start: 0.7278 (m-30) cc_final: 0.7022 (m-30) REVERT: A 930 MET cc_start: 0.7953 (ttp) cc_final: 0.7734 (ttp) REVERT: A 1090 MET cc_start: 0.7092 (ttt) cc_final: 0.6782 (ttt) REVERT: A 1110 GLN cc_start: 0.7270 (mt0) cc_final: 0.6960 (mt0) REVERT: A 1150 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7199 (mtp180) REVERT: A 1240 ARG cc_start: 0.7384 (tpt170) cc_final: 0.7065 (mmm160) REVERT: A 1352 LYS cc_start: 0.7460 (mttt) cc_final: 0.7165 (mttt) REVERT: C 460 SER cc_start: 0.7653 (p) cc_final: 0.7379 (m) outliers start: 21 outliers final: 17 residues processed: 271 average time/residue: 0.2894 time to fit residues: 108.6971 Evaluate side-chains 280 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 809 GLN A1053 HIS A1186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119083 restraints weight = 26006.502| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.58 r_work: 0.3306 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12949 Z= 0.148 Angle : 0.501 6.578 17501 Z= 0.266 Chirality : 0.040 0.153 2000 Planarity : 0.004 0.038 2212 Dihedral : 4.127 22.743 1735 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.69 % Allowed : 9.23 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.21), residues: 1566 helix: 2.37 (0.17), residues: 888 sheet: 0.90 (0.52), residues: 96 loop : -1.14 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 408 HIS 0.010 0.001 HIS A 157 PHE 0.017 0.002 PHE A 392 TYR 0.020 0.001 TYR A 516 ARG 0.006 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 708) hydrogen bonds : angle 4.11517 ( 2053) covalent geometry : bond 0.00338 (12949) covalent geometry : angle 0.50137 (17501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7223 (mtt-85) REVERT: A 50 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8181 (mtpp) REVERT: A 126 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7534 (tp-100) REVERT: A 250 ARG cc_start: 0.8161 (ttp-170) cc_final: 0.7927 (ttp80) REVERT: A 435 GLN cc_start: 0.8374 (mt0) cc_final: 0.8132 (mt0) REVERT: A 504 ASN cc_start: 0.6918 (m-40) cc_final: 0.6669 (m110) REVERT: A 522 TYR cc_start: 0.8155 (p90) cc_final: 0.7730 (p90) REVERT: A 535 LYS cc_start: 0.8115 (tppt) cc_final: 0.7864 (mmtp) REVERT: A 570 LYS cc_start: 0.8093 (mttt) cc_final: 0.7813 (mttt) REVERT: A 573 LYS cc_start: 0.7385 (mtpp) cc_final: 0.7146 (mtpp) REVERT: A 780 THR cc_start: 0.7836 (m) cc_final: 0.7578 (p) REVERT: A 803 TYR cc_start: 0.8188 (t80) cc_final: 0.7785 (t80) REVERT: A 861 VAL cc_start: 0.7622 (t) cc_final: 0.7339 (m) REVERT: A 923 ASN cc_start: 0.8346 (t0) cc_final: 0.7893 (t0) REVERT: A 925 ASP cc_start: 0.7103 (m-30) cc_final: 0.6880 (m-30) REVERT: A 930 MET cc_start: 0.7868 (ttp) cc_final: 0.7647 (ttp) REVERT: A 1019 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7270 (mtp85) REVERT: A 1090 MET cc_start: 0.6868 (ttt) cc_final: 0.6609 (ttt) REVERT: A 1110 GLN cc_start: 0.7088 (mt0) cc_final: 0.6789 (mt0) REVERT: A 1150 ARG cc_start: 0.7298 (mtm110) cc_final: 0.7060 (mtp180) REVERT: A 1240 ARG cc_start: 0.7273 (tpt170) cc_final: 0.6966 (mmm160) REVERT: A 1352 LYS cc_start: 0.7469 (mttt) cc_final: 0.7148 (mttt) REVERT: C 460 SER cc_start: 0.7628 (p) cc_final: 0.7375 (m) outliers start: 24 outliers final: 23 residues processed: 269 average time/residue: 0.2927 time to fit residues: 108.1101 Evaluate side-chains 283 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1053 HIS Chi-restraints excluded: chain A residue 1132 CYS Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain E residue 371 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 135 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 91 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 120 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 809 GLN A1053 HIS A1186 ASN D 366 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121887 restraints weight = 44282.144| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.06 r_work: 0.3188 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12949 Z= 0.133 Angle : 0.493 7.079 17501 Z= 0.260 Chirality : 0.039 0.151 2000 Planarity : 0.004 0.035 2212 Dihedral : 4.082 22.398 1735 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.69 % Allowed : 9.86 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.21), residues: 1566 helix: 2.46 (0.17), residues: 888 sheet: 0.88 (0.52), residues: 96 loop : -1.17 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 408 HIS 0.013 0.001 HIS A1053 PHE 0.024 0.001 PHE A 546 TYR 0.017 0.001 TYR A 516 ARG 0.008 0.000 ARG A1112 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 708) hydrogen bonds : angle 4.05810 ( 2053) covalent geometry : bond 0.00294 (12949) covalent geometry : angle 0.49337 (17501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7278 (mtt-85) REVERT: A 50 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8339 (mtpp) REVERT: A 126 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7542 (tp40) REVERT: A 250 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.8050 (ttp80) REVERT: A 329 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7360 (mt-10) REVERT: A 435 GLN cc_start: 0.8434 (mt0) cc_final: 0.8180 (mt0) REVERT: A 504 ASN cc_start: 0.7052 (m-40) cc_final: 0.6659 (m110) REVERT: A 522 TYR cc_start: 0.8262 (p90) cc_final: 0.7833 (p90) REVERT: A 535 LYS cc_start: 0.8198 (tppt) cc_final: 0.7954 (mmtp) REVERT: A 570 LYS cc_start: 0.8201 (mttt) cc_final: 0.7888 (mttt) REVERT: A 573 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7193 (mtpp) REVERT: A 780 THR cc_start: 0.7986 (m) cc_final: 0.7709 (p) REVERT: A 803 TYR cc_start: 0.8267 (t80) cc_final: 0.7909 (t80) REVERT: A 861 VAL cc_start: 0.7620 (t) cc_final: 0.7342 (m) REVERT: A 923 ASN cc_start: 0.8342 (t0) cc_final: 0.7869 (t0) REVERT: A 925 ASP cc_start: 0.7308 (m-30) cc_final: 0.7061 (m-30) REVERT: A 930 MET cc_start: 0.8012 (ttp) cc_final: 0.7797 (ttp) REVERT: A 1090 MET cc_start: 0.7102 (ttt) cc_final: 0.6776 (ttt) REVERT: A 1110 GLN cc_start: 0.7276 (mt0) cc_final: 0.6899 (mt0) REVERT: A 1112 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7401 (ttm-80) REVERT: A 1150 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7255 (mtp180) REVERT: A 1240 ARG cc_start: 0.7444 (tpt170) cc_final: 0.7082 (mmm160) REVERT: A 1352 LYS cc_start: 0.7563 (mttt) cc_final: 0.7228 (mttt) REVERT: D 366 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7716 (m-70) outliers start: 24 outliers final: 22 residues processed: 277 average time/residue: 0.2989 time to fit residues: 114.4829 Evaluate side-chains 283 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1132 CYS Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain D residue 366 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 89 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 130 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 809 GLN A1053 HIS A1186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116441 restraints weight = 42035.126| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.83 r_work: 0.3194 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12949 Z= 0.166 Angle : 0.524 8.436 17501 Z= 0.275 Chirality : 0.041 0.152 2000 Planarity : 0.004 0.033 2212 Dihedral : 4.144 22.332 1735 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 10.28 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.21), residues: 1566 helix: 2.38 (0.17), residues: 889 sheet: 0.79 (0.52), residues: 96 loop : -1.20 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 408 HIS 0.016 0.001 HIS D 366 PHE 0.017 0.002 PHE A 392 TYR 0.021 0.002 TYR A 516 ARG 0.007 0.000 ARG A1112 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 708) hydrogen bonds : angle 4.11661 ( 2053) covalent geometry : bond 0.00385 (12949) covalent geometry : angle 0.52355 (17501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7586 (mtt90) cc_final: 0.7373 (mtt180) REVERT: A 50 LYS cc_start: 0.8641 (ttmt) cc_final: 0.8300 (mtpp) REVERT: A 194 VAL cc_start: 0.8441 (m) cc_final: 0.8162 (t) REVERT: A 250 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.8082 (ttp80) REVERT: A 329 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 435 GLN cc_start: 0.8428 (mt0) cc_final: 0.8196 (mt0) REVERT: A 504 ASN cc_start: 0.7071 (m-40) cc_final: 0.6602 (m110) REVERT: A 535 LYS cc_start: 0.8186 (tppt) cc_final: 0.7929 (mmtp) REVERT: A 570 LYS cc_start: 0.8192 (mttt) cc_final: 0.7891 (mttt) REVERT: A 573 LYS cc_start: 0.7536 (mtpp) cc_final: 0.7262 (mtpp) REVERT: A 780 THR cc_start: 0.7975 (m) cc_final: 0.7707 (p) REVERT: A 803 TYR cc_start: 0.8277 (t80) cc_final: 0.8005 (t80) REVERT: A 861 VAL cc_start: 0.7682 (t) cc_final: 0.7405 (m) REVERT: A 923 ASN cc_start: 0.8349 (t0) cc_final: 0.7887 (t0) REVERT: A 925 ASP cc_start: 0.7317 (m-30) cc_final: 0.7092 (m-30) REVERT: A 930 MET cc_start: 0.7992 (ttp) cc_final: 0.7776 (ttp) REVERT: A 1090 MET cc_start: 0.7043 (ttt) cc_final: 0.6724 (ttt) REVERT: A 1110 GLN cc_start: 0.7245 (mt0) cc_final: 0.6886 (mt0) REVERT: A 1112 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: A 1132 CYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7678 (m) REVERT: A 1150 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7262 (mtp180) REVERT: A 1240 ARG cc_start: 0.7483 (tpt170) cc_final: 0.7112 (mmm160) REVERT: A 1352 LYS cc_start: 0.7632 (mttt) cc_final: 0.7260 (mttt) outliers start: 27 outliers final: 22 residues processed: 277 average time/residue: 0.2939 time to fit residues: 112.1146 Evaluate side-chains 282 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1132 CYS Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 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 404 HIS A 557 GLN A 681 GLN A1186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.149184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116197 restraints weight = 34804.184| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.42 r_work: 0.3233 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12949 Z= 0.185 Angle : 0.549 8.213 17501 Z= 0.287 Chirality : 0.042 0.151 2000 Planarity : 0.004 0.038 2212 Dihedral : 4.233 22.360 1735 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.90 % Allowed : 10.49 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.21), residues: 1566 helix: 2.29 (0.17), residues: 891 sheet: 0.57 (0.53), residues: 98 loop : -1.29 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 408 HIS 0.013 0.001 HIS A 157 PHE 0.024 0.002 PHE A 546 TYR 0.021 0.002 TYR A 516 ARG 0.007 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 708) hydrogen bonds : angle 4.18332 ( 2053) covalent geometry : bond 0.00437 (12949) covalent geometry : angle 0.54879 (17501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7570 (mtt90) cc_final: 0.7354 (mtt180) REVERT: A 50 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8209 (mtpp) REVERT: A 104 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7285 (mtm-85) REVERT: A 194 VAL cc_start: 0.8418 (m) cc_final: 0.8161 (t) REVERT: A 250 ARG cc_start: 0.8293 (ttp-170) cc_final: 0.8047 (ttp80) REVERT: A 329 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 435 GLN cc_start: 0.8393 (mt0) cc_final: 0.8158 (mt0) REVERT: A 535 LYS cc_start: 0.8123 (tppt) cc_final: 0.7872 (mmtp) REVERT: A 570 LYS cc_start: 0.8141 (mttt) cc_final: 0.7706 (mttt) REVERT: A 573 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7211 (mtpp) REVERT: A 780 THR cc_start: 0.7925 (m) cc_final: 0.7643 (p) REVERT: A 803 TYR cc_start: 0.8261 (t80) cc_final: 0.8019 (t80) REVERT: A 861 VAL cc_start: 0.7729 (t) cc_final: 0.7463 (m) REVERT: A 923 ASN cc_start: 0.8325 (t0) cc_final: 0.7860 (t0) REVERT: A 925 ASP cc_start: 0.7233 (m-30) cc_final: 0.7027 (m-30) REVERT: A 930 MET cc_start: 0.7949 (ttp) cc_final: 0.7726 (ttp) REVERT: A 1012 LEU cc_start: 0.7906 (mt) cc_final: 0.7651 (mm) REVERT: A 1090 MET cc_start: 0.6952 (ttt) cc_final: 0.6656 (ttt) REVERT: A 1110 GLN cc_start: 0.7162 (mt0) cc_final: 0.6883 (mt0) REVERT: A 1112 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7435 (ttp80) REVERT: A 1150 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7203 (mtp180) REVERT: A 1240 ARG cc_start: 0.7414 (tpt170) cc_final: 0.7041 (mmm160) REVERT: A 1352 LYS cc_start: 0.7689 (mttt) cc_final: 0.7311 (mttt) REVERT: A 1379 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.6124 (ttt90) REVERT: C 460 SER cc_start: 0.7605 (p) cc_final: 0.7376 (m) outliers start: 27 outliers final: 24 residues processed: 278 average time/residue: 0.3125 time to fit residues: 119.5392 Evaluate side-chains 290 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1379 ARG Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 100 optimal weight: 0.0170 chunk 112 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 681 GLN A 809 GLN A 812 HIS A1186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116924 restraints weight = 38506.325| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.61 r_work: 0.3207 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12949 Z= 0.148 Angle : 0.522 8.185 17501 Z= 0.275 Chirality : 0.040 0.153 2000 Planarity : 0.004 0.047 2212 Dihedral : 4.169 22.118 1735 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.83 % Allowed : 10.70 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.21), residues: 1566 helix: 2.37 (0.17), residues: 893 sheet: 0.56 (0.53), residues: 98 loop : -1.27 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 408 HIS 0.012 0.001 HIS A 157 PHE 0.016 0.002 PHE A 392 TYR 0.018 0.002 TYR A 516 ARG 0.011 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 708) hydrogen bonds : angle 4.11667 ( 2053) covalent geometry : bond 0.00338 (12949) covalent geometry : angle 0.52242 (17501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7576 (mtt90) cc_final: 0.7353 (mtt180) REVERT: A 50 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8270 (mtpp) REVERT: A 250 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.8066 (ttp80) REVERT: A 329 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 435 GLN cc_start: 0.8429 (mt0) cc_final: 0.8200 (mt0) REVERT: A 535 LYS cc_start: 0.8174 (tppt) cc_final: 0.7920 (mmtp) REVERT: A 570 LYS cc_start: 0.8109 (mttt) cc_final: 0.7869 (mttt) REVERT: A 573 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7254 (mtpp) REVERT: A 780 THR cc_start: 0.7950 (m) cc_final: 0.7666 (p) REVERT: A 803 TYR cc_start: 0.8254 (t80) cc_final: 0.8002 (t80) REVERT: A 861 VAL cc_start: 0.7734 (t) cc_final: 0.7465 (m) REVERT: A 923 ASN cc_start: 0.8322 (t0) cc_final: 0.7853 (t0) REVERT: A 925 ASP cc_start: 0.7263 (m-30) cc_final: 0.7047 (m-30) REVERT: A 930 MET cc_start: 0.7982 (ttp) cc_final: 0.7763 (ttp) REVERT: A 1012 LEU cc_start: 0.7932 (mt) cc_final: 0.7664 (mm) REVERT: A 1090 MET cc_start: 0.6996 (ttt) cc_final: 0.6688 (ttt) REVERT: A 1110 GLN cc_start: 0.7199 (mt0) cc_final: 0.6848 (mt0) REVERT: A 1112 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7489 (ttp80) REVERT: A 1150 ARG cc_start: 0.7532 (mtm110) cc_final: 0.7268 (mtp180) REVERT: A 1240 ARG cc_start: 0.7476 (tpt170) cc_final: 0.7122 (mmm160) REVERT: A 1352 LYS cc_start: 0.7705 (mttt) cc_final: 0.7342 (mttt) REVERT: A 1379 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6179 (ttt90) outliers start: 26 outliers final: 23 residues processed: 272 average time/residue: 0.3032 time to fit residues: 112.8784 Evaluate side-chains 287 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 263 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1379 ARG Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 142 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 123 optimal weight: 0.0020 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 681 GLN A 812 HIS A1186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120784 restraints weight = 34574.671| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.53 r_work: 0.3241 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12949 Z= 0.151 Angle : 0.533 8.140 17501 Z= 0.278 Chirality : 0.040 0.153 2000 Planarity : 0.004 0.033 2212 Dihedral : 4.161 21.941 1735 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.69 % Allowed : 11.20 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.21), residues: 1566 helix: 2.42 (0.17), residues: 891 sheet: 0.52 (0.53), residues: 98 loop : -1.27 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 408 HIS 0.012 0.001 HIS A 157 PHE 0.027 0.002 PHE A 546 TYR 0.018 0.002 TYR A 516 ARG 0.007 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 708) hydrogen bonds : angle 4.11194 ( 2053) covalent geometry : bond 0.00349 (12949) covalent geometry : angle 0.53252 (17501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3132 Ramachandran restraints generated. 1566 Oldfield, 0 Emsley, 1566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.677 Fit side-chains REVERT: A 33 ARG cc_start: 0.7557 (mtt90) cc_final: 0.7339 (mtt180) REVERT: A 50 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8216 (mtpp) REVERT: A 250 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.8029 (ttp80) REVERT: A 329 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 435 GLN cc_start: 0.8410 (mt0) cc_final: 0.8179 (mt0) REVERT: A 535 LYS cc_start: 0.8146 (tppt) cc_final: 0.7900 (mmtp) REVERT: A 570 LYS cc_start: 0.8109 (mttt) cc_final: 0.7879 (mttt) REVERT: A 573 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7246 (mtpp) REVERT: A 780 THR cc_start: 0.7893 (m) cc_final: 0.7616 (p) REVERT: A 803 TYR cc_start: 0.8261 (t80) cc_final: 0.7993 (t80) REVERT: A 861 VAL cc_start: 0.7735 (t) cc_final: 0.7476 (m) REVERT: A 923 ASN cc_start: 0.8339 (t0) cc_final: 0.7867 (t0) REVERT: A 925 ASP cc_start: 0.7194 (m-30) cc_final: 0.6991 (m-30) REVERT: A 930 MET cc_start: 0.7945 (ttp) cc_final: 0.7726 (ttp) REVERT: A 1012 LEU cc_start: 0.7895 (mt) cc_final: 0.7663 (mm) REVERT: A 1090 MET cc_start: 0.6915 (ttt) cc_final: 0.6624 (ttt) REVERT: A 1110 GLN cc_start: 0.7149 (mt0) cc_final: 0.6879 (mt0) REVERT: A 1112 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: A 1150 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7215 (mtp180) REVERT: A 1240 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7103 (mmm160) REVERT: A 1352 LYS cc_start: 0.7707 (mttt) cc_final: 0.7344 (mttt) REVERT: A 1392 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7173 (mt) outliers start: 24 outliers final: 22 residues processed: 271 average time/residue: 0.2913 time to fit residues: 108.9346 Evaluate side-chains 284 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain C residue 462 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 109 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 404 HIS A 681 GLN A 809 GLN A 812 HIS A1186 ASN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121471 restraints weight = 48923.858| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.99 r_work: 0.3183 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12949 Z= 0.137 Angle : 0.516 8.019 17501 Z= 0.271 Chirality : 0.040 0.153 2000 Planarity : 0.004 0.033 2212 Dihedral : 4.112 21.690 1735 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.55 % Allowed : 11.48 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.21), residues: 1566 helix: 2.47 (0.17), residues: 893 sheet: 0.52 (0.53), residues: 98 loop : -1.25 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 408 HIS 0.011 0.001 HIS A 157 PHE 0.017 0.001 PHE A 392 TYR 0.016 0.001 TYR A 516 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 708) hydrogen bonds : angle 4.06659 ( 2053) covalent geometry : bond 0.00310 (12949) covalent geometry : angle 0.51619 (17501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7184.84 seconds wall clock time: 124 minutes 55.26 seconds (7495.26 seconds total)