Starting phenix.real_space_refine on Thu Aug 6 01:03:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vuj_65365/08_2026/9vuj_65365.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 65 5.16 5 C 7811 2.51 5 N 2115 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12245 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 2 Chain: "B" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 262 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain: "D" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 317 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "L" Number of atoms: 10167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1266, 10155 Classifications: {'peptide': 1266} Link IDs: {'PTRANS': 53, 'TRANS': 1212} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 1266, 10155 Classifications: {'peptide': 1266} Link IDs: {'PTRANS': 53, 'TRANS': 1212} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 10368 Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10812 SG CYS L1177 75.430 75.295 31.350 1.00 65.47 S ATOM 10833 SG CYS L1180 74.903 78.868 32.613 1.00 63.79 S ATOM 10446 SG CYS L1132 53.803 78.842 24.211 1.00 76.22 S ATOM 11956 SG CYS L1369 57.182 80.004 24.027 1.00112.33 S ATOM 11962 SG CYS L1370 55.249 78.796 27.063 1.00100.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR L1333 " occ=0.70 ... (22 atoms not shown) pdb=" OH BTYR L1333 " occ=0.30 Time building chain proxies: 4.31, per 1000 atoms: 0.35 Number of scatterers: 12245 At special positions: 0 Unit cell: (95.312, 109.779, 146.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 65 16.00 O 2251 8.00 N 2115 7.00 C 7811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 824.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L4001 " pdb="ZN ZN L4001 " - pdb=" ND1 HIS L1362 " pdb="ZN ZN L4001 " - pdb=" NE2 HIS L1364 " pdb="ZN ZN L4001 " - pdb=" SG CYS L1180 " pdb="ZN ZN L4001 " - pdb=" SG CYS L1177 " pdb=" ZN L4002 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1369 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1370 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1132 " pdb=" ZN L4003 " pdb="ZN ZN L4003 " - pdb=" NE2 HIS L 812 " pdb="ZN ZN L4003 " - pdb=" NE2 HIS L 817 " Number of angles added : 2 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 62.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 341 through 370 removed outlier: 4.160A pdb=" N GLU A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.340A pdb=" N GLU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 4.024A pdb=" N ARG A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.818A pdb=" N ASP A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 506 removed outlier: 4.181A pdb=" N MET A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 371 removed outlier: 4.173A pdb=" N SER B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 374 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'D' and resid 342 through 369 Processing helix chain 'L' and resid 22 through 32 Processing helix chain 'L' and resid 43 through 56 Processing helix chain 'L' and resid 59 through 76 Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'L' and resid 87 through 89 No H-bonds generated for 'chain 'L' and resid 87 through 89' Processing helix chain 'L' and resid 90 through 95 Processing helix chain 'L' and resid 103 through 119 removed outlier: 3.713A pdb=" N LYS L 119 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 135 Processing helix chain 'L' and resid 144 through 151 removed outlier: 3.509A pdb=" N LYS L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 158 Processing helix chain 'L' and resid 161 through 182 Processing helix chain 'L' and resid 224 through 248 Processing helix chain 'L' and resid 251 through 273 removed outlier: 4.453A pdb=" N GLY L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY L 267 " --> pdb=" O LYS L 263 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE L 269 " --> pdb=" O ILE L 265 " (cutoff:3.500A) Proline residue: L 270 - end of helix Processing helix chain 'L' and resid 275 through 282 removed outlier: 4.054A pdb=" N ILE L 279 " --> pdb=" O PRO L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 293 removed outlier: 3.843A pdb=" N SER L 287 " --> pdb=" O LEU L 283 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 302 through 320 removed outlier: 4.137A pdb=" N HIS L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN L 319 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY L 320 " --> pdb=" O LEU L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 339 removed outlier: 3.597A pdb=" N TYR L 327 " --> pdb=" O ASP L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 346 Processing helix chain 'L' and resid 347 through 355 removed outlier: 4.137A pdb=" N ARG L 354 " --> pdb=" O SER L 351 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER L 355 " --> pdb=" O PHE L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 375 removed outlier: 3.781A pdb=" N ALA L 366 " --> pdb=" O GLU L 362 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR L 373 " --> pdb=" O ASN L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 404 Processing helix chain 'L' and resid 418 through 428 Processing helix chain 'L' and resid 432 through 439 Processing helix chain 'L' and resid 440 through 444 Processing helix chain 'L' and resid 459 through 464 removed outlier: 4.317A pdb=" N MET L 462 " --> pdb=" O ASP L 459 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR L 463 " --> pdb=" O LEU L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.962A pdb=" N TRP L 476 " --> pdb=" O GLN L 473 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP L 477 " --> pdb=" O ARG L 474 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL L 479 " --> pdb=" O TRP L 476 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR L 480 " --> pdb=" O ASP L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 504 Processing helix chain 'L' and resid 509 through 519 removed outlier: 3.842A pdb=" N VAL L 517 " --> pdb=" O VAL L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 567 Processing helix chain 'L' and resid 568 through 574 removed outlier: 4.078A pdb=" N ASP L 574 " --> pdb=" O TYR L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 671 removed outlier: 3.803A pdb=" N TRP L 671 " --> pdb=" O CYS L 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 672 through 688 removed outlier: 5.486A pdb=" N LEU L 678 " --> pdb=" O GLU L 674 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE L 679 " --> pdb=" O THR L 675 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 701 removed outlier: 3.681A pdb=" N LYS L 698 " --> pdb=" O GLN L 694 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 725 removed outlier: 3.693A pdb=" N VAL L 725 " --> pdb=" O LEU L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 743 through 763 removed outlier: 3.512A pdb=" N ILE L 752 " --> pdb=" O THR L 748 " (cutoff:3.500A) Proline residue: L 753 - end of helix Processing helix chain 'L' and resid 788 through 814 removed outlier: 3.535A pdb=" N LYS L 792 " --> pdb=" O PRO L 788 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE L 814 " --> pdb=" O ARG L 810 " (cutoff:3.500A) Processing helix chain 'L' and resid 819 through 823 Processing helix chain 'L' and resid 849 through 853 Processing helix chain 'L' and resid 863 through 881 removed outlier: 3.660A pdb=" N ALA L 867 " --> pdb=" O GLU L 863 " (cutoff:3.500A) Processing helix chain 'L' and resid 886 through 906 Processing helix chain 'L' and resid 913 through 922 Proline residue: L 919 - end of helix Processing helix chain 'L' and resid 923 through 933 removed outlier: 3.873A pdb=" N LEU L 927 " --> pdb=" O ASN L 923 " (cutoff:3.500A) Processing helix chain 'L' and resid 934 through 938 Processing helix chain 'L' and resid 944 through 949 Processing helix chain 'L' and resid 955 through 970 Processing helix chain 'L' and resid 975 through 982 removed outlier: 4.263A pdb=" N HIS L 979 " --> pdb=" O GLU L 975 " (cutoff:3.500A) Processing helix chain 'L' and resid 990 through 997 Processing helix chain 'L' and resid 1008 through 1024 removed outlier: 3.510A pdb=" N HIS L1024 " --> pdb=" O PHE L1020 " (cutoff:3.500A) Processing helix chain 'L' and resid 1027 through 1031 removed outlier: 3.595A pdb=" N LYS L1031 " --> pdb=" O PRO L1028 " (cutoff:3.500A) Processing helix chain 'L' and resid 1037 through 1051 Processing helix chain 'L' and resid 1056 through 1066 Processing helix chain 'L' and resid 1067 through 1079 Processing helix chain 'L' and resid 1082 through 1092 Processing helix chain 'L' and resid 1096 through 1105 Processing helix chain 'L' and resid 1105 through 1120 Processing helix chain 'L' and resid 1132 through 1145 Processing helix chain 'L' and resid 1145 through 1150 Processing helix chain 'L' and resid 1161 through 1165 Processing helix chain 'L' and resid 1177 through 1183 removed outlier: 3.609A pdb=" N GLY L1183 " --> pdb=" O ILE L1179 " (cutoff:3.500A) Processing helix chain 'L' and resid 1232 through 1249 Processing helix chain 'L' and resid 1252 through 1264 Processing helix chain 'L' and resid 1270 through 1278 Processing helix chain 'L' and resid 1304 through 1309 removed outlier: 3.973A pdb=" N ARG L1309 " --> pdb=" O VAL L1305 " (cutoff:3.500A) Processing helix chain 'L' and resid 1330 through 1348 Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 372 removed outlier: 7.811A pdb=" N ALA D 373 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 398 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 20 through 21 removed outlier: 6.855A pdb=" N ILE L 20 " --> pdb=" O LEU L 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 83 through 84 removed outlier: 6.241A pdb=" N SER L 83 " --> pdb=" O VAL L 220 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR L 222 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS L 219 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 213 " --> pdb=" O GLU L 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 411 through 412 Processing sheet with id=AA5, first strand: chain 'L' and resid 545 through 549 removed outlier: 4.965A pdb=" N LEU L 530 " --> pdb=" O VAL L 704 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR L 706 " --> pdb=" O LEU L 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 765 through 770 removed outlier: 3.583A pdb=" N ARG L 765 " --> pdb=" O THR L 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 830 through 831 removed outlier: 3.509A pdb=" N PHE L 830 " --> pdb=" O TYR L 837 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1166 through 1171 666 hydrogen bonds defined for protein. 1888 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: 2.30 Time building geometry restraints manager: 1.24 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: 3979 1.34 - 1.46: 2690 1.46 - 1.58: 5711 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 12487 Sorted by residual: bond pdb=" CB ASP L 42 " pdb=" CG ASP L 42 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 bond pdb=" CB VAL A 463 " pdb=" CG2 VAL A 463 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" C ASP L 988 " pdb=" O ASP L 988 " ideal model delta sigma weight residual 1.235 1.221 0.014 1.19e-02 7.06e+03 1.46e+00 bond pdb=" C PHE L 991 " pdb=" O PHE L 991 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.17e-02 7.31e+03 1.45e+00 bond pdb=" CA GLY L 954 " pdb=" C GLY L 954 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.41e+00 ... (remaining 12482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 16670 2.41 - 4.81: 200 4.81 - 7.22: 17 7.22 - 9.63: 2 9.63 - 12.03: 1 Bond angle restraints: 16890 Sorted by residual: angle pdb=" C GLY A 457 " pdb=" N PRO A 458 " pdb=" CA PRO A 458 " ideal model delta sigma weight residual 119.05 127.92 -8.87 1.11e+00 8.12e-01 6.38e+01 angle pdb=" C VAL A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta sigma weight residual 119.78 124.50 -4.72 1.03e+00 9.43e-01 2.10e+01 angle pdb=" C PRO L 934 " pdb=" N ALA L 935 " pdb=" CA ALA L 935 " ideal model delta sigma weight residual 120.09 125.65 -5.56 1.25e+00 6.40e-01 1.98e+01 angle pdb=" CB MET L 61 " pdb=" CG MET L 61 " pdb=" SD MET L 61 " ideal model delta sigma weight residual 112.70 124.73 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" N GLY L 406 " pdb=" CA GLY L 406 " pdb=" C GLY L 406 " ideal model delta sigma weight residual 113.58 116.96 -3.38 1.07e+00 8.73e-01 1.00e+01 ... (remaining 16885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 6596 17.13 - 34.26: 753 34.26 - 51.40: 192 51.40 - 68.53: 36 68.53 - 85.66: 9 Dihedral angle restraints: 7586 sinusoidal: 3101 harmonic: 4485 Sorted by residual: dihedral pdb=" CA TYR L1249 " pdb=" C TYR L1249 " pdb=" N GLY L1250 " pdb=" CA GLY L1250 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA HIS L 416 " pdb=" C HIS L 416 " pdb=" N ALA L 417 " pdb=" CA ALA L 417 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA LEU L1386 " pdb=" C LEU L1386 " pdb=" N GLU L1387 " pdb=" CA GLU L1387 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 7583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1192 0.032 - 0.064: 529 0.064 - 0.096: 136 0.096 - 0.128: 57 0.128 - 0.160: 9 Chirality restraints: 1923 Sorted by residual: chirality pdb=" CA TYR L 87 " pdb=" N TYR L 87 " pdb=" C TYR L 87 " pdb=" CB TYR L 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA ILE L 732 " pdb=" N ILE L 732 " pdb=" C ILE L 732 " pdb=" CB ILE L 732 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ALA A 459 " pdb=" N ALA A 459 " pdb=" C ALA A 459 " pdb=" CB ALA A 459 " both_signs ideal model delta sigma weight residual False 2.48 2.35 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1920 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 787 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.90e+00 pdb=" N PRO L 788 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 788 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 788 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 453 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO A 454 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 284 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO L 285 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 285 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 285 " 0.026 5.00e-02 4.00e+02 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1904 2.76 - 3.29: 11336 3.29 - 3.83: 19714 3.83 - 4.36: 22986 4.36 - 4.90: 40497 Nonbonded interactions: 96437 Sorted by model distance: nonbonded pdb=" OH TYR L 516 " pdb=" OD2 ASP L 525 " model vdw 2.223 3.040 nonbonded pdb=" NE2 HIS L 15 " pdb=" O TRP L 856 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU D 364 " pdb=" NZ LYS L 441 " model vdw 2.245 3.120 nonbonded pdb=" OG1 THR L 859 " pdb=" O VAL L 861 " model vdw 2.270 3.040 nonbonded pdb=" O ILE A 468 " pdb=" OG SER A 471 " model vdw 2.301 3.040 ... (remaining 96432 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=0.30 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 0.047 12496 Z= 0.168 Angle : 0.652 12.032 16892 Z= 0.370 Chirality : 0.041 0.160 1923 Planarity : 0.005 0.055 2139 Dihedral : 15.509 85.659 4688 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.88 % Allowed : 17.96 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.22), residues: 1515 helix: 1.79 (0.18), residues: 833 sheet: 0.19 (0.56), residues: 104 loop : -1.03 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L1112 TYR 0.022 0.002 TYR L1310 PHE 0.023 0.002 PHE L 392 TRP 0.011 0.002 TRP L 695 HIS 0.012 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (12487) covalent geometry : angle 0.65075 / 0.37 (16890) hydrogen bonds : bond 0.15678 / 10.39 ( 666) hydrogen bonds : angle 4.93439 / 3.64 ( 1888) metal coordination : bond 0.01592 / 0.56 ( 9) metal coordination : angle 4.26765 / 2.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 476 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6894 (p0) REVERT: L 61 MET cc_start: 0.6450 (mmm) cc_final: 0.5316 (ttp) REVERT: L 100 LYS cc_start: 0.7415 (ttmm) cc_final: 0.7030 (mmtt) REVERT: L 111 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7618 (mtmp) REVERT: L 130 ASP cc_start: 0.7737 (m-30) cc_final: 0.7506 (m-30) REVERT: L 314 ASP cc_start: 0.7586 (t0) cc_final: 0.7350 (t0) REVERT: L 657 SER cc_start: 0.8423 (p) cc_final: 0.8128 (t) REVERT: L 662 THR cc_start: 0.7785 (p) cc_final: 0.7574 (m) REVERT: L 791 LEU cc_start: 0.7474 (mp) cc_final: 0.7260 (mm) REVERT: L 997 ASP cc_start: 0.7621 (t0) cc_final: 0.7280 (t0) REVERT: L 1016 ILE cc_start: 0.7801 (mt) cc_final: 0.7501 (mt) REVERT: L 1037 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.5839 (t70) REVERT: L 1112 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7316 (ttp-110) REVERT: L 1138 ARG cc_start: 0.6641 (mmm-85) cc_final: 0.6115 (mtm-85) REVERT: L 1275 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7267 (mtp180) outliers start: 12 outliers final: 4 residues processed: 230 average time/residue: 0.6631 time to fit residues: 164.8919 Evaluate side-chains 172 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 790 ASN Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 1037 ASP Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 GLN L 358 HIS L 775 GLN L 898 GLN L1135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.208804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174104 restraints weight = 14838.689| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 1.85 r_work: 0.3874 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12496 Z= 0.138 Angle : 0.579 8.648 16892 Z= 0.303 Chirality : 0.041 0.150 1923 Planarity : 0.005 0.056 2139 Dihedral : 4.728 40.129 1690 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.37 % Allowed : 16.72 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.22), residues: 1515 helix: 2.10 (0.18), residues: 824 sheet: 0.47 (0.56), residues: 104 loop : -0.85 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L1150 TYR 0.021 0.002 TYR L 742 PHE 0.024 0.002 PHE L 392 TRP 0.010 0.001 TRP L1189 HIS 0.006 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12487) covalent geometry : angle 0.57820 / 0.30 (16890) hydrogen bonds : bond 0.05427 / 3.62 ( 666) hydrogen bonds : angle 3.99725 / 2.94 ( 1888) metal coordination : bond 0.01215 / 0.47 ( 9) metal coordination : angle 2.79857 / 1.60 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.521 Fit side-chains REVERT: A 408 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: A 409 VAL cc_start: 0.6188 (OUTLIER) cc_final: 0.5506 (m) REVERT: L 61 MET cc_start: 0.6621 (mmm) cc_final: 0.5464 (ttp) REVERT: L 263 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7712 (ttpp) REVERT: L 345 LEU cc_start: 0.7795 (mt) cc_final: 0.7584 (mm) REVERT: L 354 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6814 (mmt90) REVERT: L 447 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7806 (tttm) REVERT: L 654 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7025 (mp0) REVERT: L 657 SER cc_start: 0.8393 (p) cc_final: 0.8052 (t) REVERT: L 666 LYS cc_start: 0.8245 (tppp) cc_final: 0.7956 (tptt) REVERT: L 700 LEU cc_start: 0.8086 (mp) cc_final: 0.7869 (mt) REVERT: L 1016 ILE cc_start: 0.7659 (mt) cc_final: 0.7413 (mt) REVERT: L 1112 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7602 (ttp-110) REVERT: L 1122 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7800 (mtmp) REVERT: L 1138 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6753 (mtm110) REVERT: L 1275 ARG cc_start: 0.7495 (tpp-160) cc_final: 0.6938 (mtp180) REVERT: L 1345 GLU cc_start: 0.7621 (tm-30) cc_final: 0.6815 (tp30) outliers start: 46 outliers final: 13 residues processed: 214 average time/residue: 0.6897 time to fit residues: 159.4693 Evaluate side-chains 188 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 322 SER Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1122 LYS Chi-restraints excluded: chain L residue 1142 SER Chi-restraints excluded: chain L residue 1254 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 729 GLN L 979 HIS L1035 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.209243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.173808 restraints weight = 13480.765| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.63 r_work: 0.3886 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12496 Z= 0.119 Angle : 0.545 13.253 16892 Z= 0.283 Chirality : 0.040 0.148 1923 Planarity : 0.004 0.053 2139 Dihedral : 4.466 44.270 1683 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.42 % Allowed : 18.11 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1515 helix: 2.28 (0.18), residues: 824 sheet: 0.67 (0.56), residues: 104 loop : -0.69 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L1150 TYR 0.020 0.001 TYR L1310 PHE 0.021 0.001 PHE L 392 TRP 0.009 0.001 TRP L1189 HIS 0.006 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12487) covalent geometry : angle 0.54444 / 0.28 (16890) hydrogen bonds : bond 0.04768 / 3.17 ( 666) hydrogen bonds : angle 3.82877 / 2.81 ( 1888) metal coordination : bond 0.01182 / 0.44 ( 9) metal coordination : angle 2.71866 / 1.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.515 Fit side-chains REVERT: A 408 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: A 409 VAL cc_start: 0.6120 (t) cc_final: 0.5473 (m) REVERT: A 502 MET cc_start: 0.7779 (mtm) cc_final: 0.7570 (mtt) REVERT: L 61 MET cc_start: 0.6525 (mmm) cc_final: 0.5427 (ttp) REVERT: L 263 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7744 (ttpp) REVERT: L 335 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7629 (t0) REVERT: L 354 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6795 (mmt90) REVERT: L 447 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7791 (tttm) REVERT: L 654 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7053 (mp0) REVERT: L 666 LYS cc_start: 0.8215 (tppp) cc_final: 0.7935 (tptt) REVERT: L 700 LEU cc_start: 0.8082 (mp) cc_final: 0.7820 (mt) REVERT: L 1016 ILE cc_start: 0.7700 (mt) cc_final: 0.7470 (mt) REVERT: L 1107 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6796 (m-30) REVERT: L 1112 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7547 (ttp-110) REVERT: L 1275 ARG cc_start: 0.7495 (tpp-160) cc_final: 0.6916 (mtp180) REVERT: L 1345 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6768 (tp30) outliers start: 33 outliers final: 14 residues processed: 198 average time/residue: 0.6528 time to fit residues: 140.1885 Evaluate side-chains 185 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 322 SER Chi-restraints excluded: chain L residue 335 ASP Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 845 GLN L1035 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.209343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.173001 restraints weight = 16396.233| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.20 r_work: 0.3871 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12496 Z= 0.118 Angle : 0.544 12.121 16892 Z= 0.281 Chirality : 0.040 0.148 1923 Planarity : 0.004 0.052 2139 Dihedral : 4.415 44.451 1683 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.20 % Allowed : 17.82 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1515 helix: 2.33 (0.18), residues: 825 sheet: 0.85 (0.57), residues: 102 loop : -0.67 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L1150 TYR 0.020 0.001 TYR L1310 PHE 0.021 0.001 PHE L 392 TRP 0.009 0.001 TRP L1189 HIS 0.006 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (12487) covalent geometry : angle 0.54334 / 0.28 (16890) hydrogen bonds : bond 0.04628 / 3.07 ( 666) hydrogen bonds : angle 3.75071 / 2.75 ( 1888) metal coordination : bond 0.01315 / 0.50 ( 9) metal coordination : angle 3.19869 / 1.79 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.516 Fit side-chains REVERT: A 408 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: A 409 VAL cc_start: 0.6094 (t) cc_final: 0.5437 (m) REVERT: A 499 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6282 (mt0) REVERT: L 61 MET cc_start: 0.6598 (mmm) cc_final: 0.5472 (ttp) REVERT: L 335 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7582 (t0) REVERT: L 354 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6829 (mmt90) REVERT: L 447 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7786 (tttm) REVERT: L 654 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7092 (mp0) REVERT: L 666 LYS cc_start: 0.8183 (tppp) cc_final: 0.7923 (tptt) REVERT: L 700 LEU cc_start: 0.8086 (mp) cc_final: 0.7831 (mt) REVERT: L 1107 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: L 1112 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7573 (ttp-110) REVERT: L 1138 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6847 (mtm-85) REVERT: L 1271 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6697 (tm) REVERT: L 1345 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6786 (tp30) outliers start: 30 outliers final: 13 residues processed: 192 average time/residue: 0.6557 time to fit residues: 135.7191 Evaluate side-chains 184 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 335 ASP Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1271 LEU Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.209903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.173887 restraints weight = 20048.978| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.57 r_work: 0.3840 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12496 Z= 0.114 Angle : 0.535 11.525 16892 Z= 0.276 Chirality : 0.040 0.148 1923 Planarity : 0.004 0.051 2139 Dihedral : 4.380 44.302 1683 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.98 % Allowed : 18.11 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.22), residues: 1515 helix: 2.42 (0.18), residues: 825 sheet: 0.85 (0.57), residues: 102 loop : -0.63 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L1150 TYR 0.020 0.001 TYR L1310 PHE 0.020 0.001 PHE L 392 TRP 0.012 0.001 TRP L1189 HIS 0.005 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (12487) covalent geometry : angle 0.53429 / 0.28 (16890) hydrogen bonds : bond 0.04393 / 2.90 ( 666) hydrogen bonds : angle 3.71244 / 2.71 ( 1888) metal coordination : bond 0.01248 / 0.48 ( 9) metal coordination : angle 3.19101 / 1.78 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.315 Fit side-chains REVERT: A 408 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: A 409 VAL cc_start: 0.6062 (t) cc_final: 0.5337 (m) REVERT: L 61 MET cc_start: 0.6644 (mmm) cc_final: 0.5436 (ttp) REVERT: L 263 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7828 (ttpp) REVERT: L 335 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7579 (t0) REVERT: L 447 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: L 654 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6893 (mp0) REVERT: L 666 LYS cc_start: 0.8174 (tppp) cc_final: 0.7898 (tptt) REVERT: L 1107 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: L 1112 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7448 (ttp-110) REVERT: L 1138 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6707 (mtm-85) REVERT: L 1271 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6469 (tm) REVERT: L 1345 GLU cc_start: 0.7600 (tm-30) cc_final: 0.6861 (mm-30) outliers start: 27 outliers final: 12 residues processed: 186 average time/residue: 0.5576 time to fit residues: 112.4659 Evaluate side-chains 179 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 335 ASP Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1271 LEU Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 100 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 136 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.207367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.170663 restraints weight = 19583.600| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.52 r_work: 0.3798 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12496 Z= 0.137 Angle : 0.575 11.019 16892 Z= 0.296 Chirality : 0.041 0.150 1923 Planarity : 0.004 0.052 2139 Dihedral : 4.495 43.632 1683 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.42 % Allowed : 18.33 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.22), residues: 1515 helix: 2.30 (0.18), residues: 825 sheet: 0.81 (0.56), residues: 102 loop : -0.63 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L1150 TYR 0.020 0.002 TYR L1310 PHE 0.024 0.002 PHE L 392 TRP 0.012 0.001 TRP L1189 HIS 0.007 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12487) covalent geometry : angle 0.57273 / 0.30 (16890) hydrogen bonds : bond 0.05031 / 3.33 ( 666) hydrogen bonds : angle 3.77033 / 2.75 ( 1888) metal coordination : bond 0.01572 / 0.60 ( 9) metal coordination : angle 4.24109 / 2.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 408 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: A 409 VAL cc_start: 0.6009 (OUTLIER) cc_final: 0.5364 (m) REVERT: A 446 MET cc_start: 0.5650 (tpt) cc_final: 0.5412 (tpp) REVERT: A 499 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6299 (mt0) REVERT: L 61 MET cc_start: 0.6407 (mmm) cc_final: 0.5335 (ttp) REVERT: L 447 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: L 654 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6791 (mp0) REVERT: L 657 SER cc_start: 0.8306 (p) cc_final: 0.8047 (t) REVERT: L 666 LYS cc_start: 0.8192 (tppp) cc_final: 0.7945 (tptt) REVERT: L 985 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: L 1107 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6816 (m-30) REVERT: L 1112 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7349 (ttp-110) REVERT: L 1138 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6652 (mtm110) REVERT: L 1271 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6397 (tm) REVERT: L 1345 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6886 (mm-30) outliers start: 33 outliers final: 15 residues processed: 186 average time/residue: 0.5963 time to fit residues: 119.9721 Evaluate side-chains 187 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 322 SER Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 824 ILE Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 985 GLN Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1271 LEU Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 319 ASN L 870 ASN L1035 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.209031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.173872 restraints weight = 14857.673| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.81 r_work: 0.3880 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12496 Z= 0.117 Angle : 0.538 10.728 16892 Z= 0.278 Chirality : 0.040 0.148 1923 Planarity : 0.004 0.051 2139 Dihedral : 4.411 44.525 1683 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.27 % Allowed : 18.55 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.22), residues: 1515 helix: 2.40 (0.18), residues: 825 sheet: 0.76 (0.56), residues: 102 loop : -0.56 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L1150 TYR 0.020 0.001 TYR L1310 PHE 0.020 0.001 PHE L 392 TRP 0.012 0.001 TRP L1189 HIS 0.006 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12487) covalent geometry : angle 0.53649 / 0.28 (16890) hydrogen bonds : bond 0.04479 / 2.97 ( 666) hydrogen bonds : angle 3.70274 / 2.70 ( 1888) metal coordination : bond 0.01280 / 0.49 ( 9) metal coordination : angle 3.44943 / 1.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 408 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: A 409 VAL cc_start: 0.6097 (t) cc_final: 0.5425 (m) REVERT: A 446 MET cc_start: 0.5748 (tpt) cc_final: 0.5449 (tpp) REVERT: L 61 MET cc_start: 0.6537 (mmm) cc_final: 0.5428 (ttp) REVERT: L 335 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7698 (t0) REVERT: L 368 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.5902 (mp0) REVERT: L 447 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7796 (tttm) REVERT: L 540 LYS cc_start: 0.7835 (mptp) cc_final: 0.7266 (mppt) REVERT: L 654 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6975 (mp0) REVERT: L 657 SER cc_start: 0.8431 (p) cc_final: 0.8067 (t) REVERT: L 666 LYS cc_start: 0.8198 (tppp) cc_final: 0.7950 (tptt) REVERT: L 985 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: L 1107 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: L 1112 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7453 (ttp-110) REVERT: L 1138 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6743 (mtm110) REVERT: L 1271 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6525 (tm) REVERT: L 1345 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6971 (mm-30) outliers start: 31 outliers final: 14 residues processed: 185 average time/residue: 0.6492 time to fit residues: 129.9277 Evaluate side-chains 185 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 322 SER Chi-restraints excluded: chain L residue 335 ASP Chi-restraints excluded: chain L residue 368 GLU Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 768 SER Chi-restraints excluded: chain L residue 783 VAL Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 985 GLN Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1271 LEU Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 136 optimal weight: 0.0970 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.210116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173276 restraints weight = 20132.898| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.36 r_work: 0.3827 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12496 Z= 0.107 Angle : 0.519 10.537 16892 Z= 0.268 Chirality : 0.039 0.148 1923 Planarity : 0.004 0.052 2139 Dihedral : 4.147 43.979 1681 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.05 % Allowed : 18.77 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1515 helix: 2.53 (0.18), residues: 824 sheet: 0.70 (0.55), residues: 102 loop : -0.49 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L1150 TYR 0.020 0.001 TYR L1310 PHE 0.019 0.001 PHE L 392 TRP 0.013 0.001 TRP L1189 HIS 0.005 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12487) covalent geometry : angle 0.51822 / 0.27 (16890) hydrogen bonds : bond 0.04074 / 2.71 ( 666) hydrogen bonds : angle 3.61470 / 2.63 ( 1888) metal coordination : bond 0.01203 / 0.47 ( 9) metal coordination : angle 3.30565 / 1.84 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.499 Fit side-chains REVERT: A 408 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: A 409 VAL cc_start: 0.5841 (t) cc_final: 0.5241 (m) REVERT: L 61 MET cc_start: 0.6371 (mmm) cc_final: 0.5310 (ttp) REVERT: L 335 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7698 (t0) REVERT: L 447 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7783 (tttm) REVERT: L 540 LYS cc_start: 0.7812 (mptp) cc_final: 0.7255 (mppt) REVERT: L 654 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6928 (mp0) REVERT: L 657 SER cc_start: 0.8390 (p) cc_final: 0.8003 (t) REVERT: L 666 LYS cc_start: 0.8146 (tppp) cc_final: 0.7910 (tptt) REVERT: L 985 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: L 1107 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: L 1112 ARG cc_start: 0.7853 (mtm110) cc_final: 0.7321 (ttp-110) REVERT: L 1138 ARG cc_start: 0.6952 (mtm-85) cc_final: 0.6580 (mtm110) REVERT: L 1271 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6424 (tm) REVERT: L 1345 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6813 (mm-30) outliers start: 28 outliers final: 14 residues processed: 197 average time/residue: 0.6851 time to fit residues: 145.8507 Evaluate side-chains 190 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 322 SER Chi-restraints excluded: chain L residue 335 ASP Chi-restraints excluded: chain L residue 391 ILE Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 783 VAL Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 874 THR Chi-restraints excluded: chain L residue 927 LEU Chi-restraints excluded: chain L residue 985 GLN Chi-restraints excluded: chain L residue 1107 ASP Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1271 LEU Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.0050 chunk 8 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 0.0060 overall best weight: 0.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.214228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179099 restraints weight = 25708.775| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 4.86 r_work: 0.3825 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12496 Z= 0.097 Angle : 0.522 10.821 16892 Z= 0.264 Chirality : 0.039 0.167 1923 Planarity : 0.004 0.051 2139 Dihedral : 3.943 42.101 1681 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.32 % Allowed : 19.79 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.22), residues: 1515 helix: 2.70 (0.18), residues: 826 sheet: 0.59 (0.55), residues: 100 loop : -0.36 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L1150 TYR 0.019 0.001 TYR L1310 PHE 0.017 0.001 PHE L 392 TRP 0.018 0.001 TRP L1189 HIS 0.004 0.000 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (12487) covalent geometry : angle 0.52120 / 0.26 (16890) hydrogen bonds : bond 0.03308 / 2.21 ( 666) hydrogen bonds : angle 3.51379 / 2.55 ( 1888) metal coordination : bond 0.00870 / 0.35 ( 9) metal coordination : angle 2.49122 / 1.42 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.403 Fit side-chains REVERT: A 408 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: A 409 VAL cc_start: 0.5615 (t) cc_final: 0.4965 (m) REVERT: A 446 MET cc_start: 0.5636 (tpt) cc_final: 0.5351 (tpp) REVERT: L 61 MET cc_start: 0.6356 (mmm) cc_final: 0.5202 (ttp) REVERT: L 447 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7780 (tttm) REVERT: L 654 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7083 (mp0) REVERT: L 657 SER cc_start: 0.8460 (p) cc_final: 0.8042 (t) REVERT: L 666 LYS cc_start: 0.8117 (tppp) cc_final: 0.7833 (tptt) REVERT: L 930 MET cc_start: 0.8036 (ttm) cc_final: 0.7811 (ttt) REVERT: L 1112 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7153 (ttp-110) REVERT: L 1138 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6405 (mtm110) REVERT: L 1186 ASN cc_start: 0.6924 (m-40) cc_final: 0.6636 (m-40) REVERT: L 1345 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6555 (mm-30) outliers start: 18 outliers final: 6 residues processed: 184 average time/residue: 0.6581 time to fit residues: 131.0633 Evaluate side-chains 171 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 790 ASN Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.208251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171158 restraints weight = 18948.330| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.14 r_work: 0.3806 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12496 Z= 0.139 Angle : 0.592 10.898 16892 Z= 0.303 Chirality : 0.041 0.153 1923 Planarity : 0.004 0.051 2139 Dihedral : 4.237 44.499 1681 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.03 % Allowed : 20.60 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1515 helix: 2.41 (0.18), residues: 826 sheet: 0.79 (0.55), residues: 102 loop : -0.45 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L1150 TYR 0.020 0.002 TYR L1310 PHE 0.023 0.002 PHE L 392 TRP 0.015 0.001 TRP L1189 HIS 0.007 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12487) covalent geometry : angle 0.59008 / 0.30 (16890) hydrogen bonds : bond 0.04849 / 3.20 ( 666) hydrogen bonds : angle 3.72962 / 2.70 ( 1888) metal coordination : bond 0.01675 / 0.64 ( 9) metal coordination : angle 4.90722 / 2.67 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.297 Fit side-chains REVERT: A 408 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: A 446 MET cc_start: 0.5769 (tpt) cc_final: 0.5419 (tpp) REVERT: L 61 MET cc_start: 0.6421 (mmm) cc_final: 0.5377 (ttp) REVERT: L 354 ARG cc_start: 0.7174 (mtp180) cc_final: 0.6943 (ppt90) REVERT: L 447 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7809 (tttm) REVERT: L 654 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7002 (mp0) REVERT: L 666 LYS cc_start: 0.8169 (tppp) cc_final: 0.7938 (tptt) REVERT: L 1112 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7365 (ttp-110) REVERT: L 1138 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6675 (mtm110) REVERT: L 1199 ASP cc_start: 0.6358 (t70) cc_final: 0.6130 (t70) REVERT: L 1345 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6813 (mm-30) outliers start: 14 outliers final: 6 residues processed: 176 average time/residue: 0.6143 time to fit residues: 116.4386 Evaluate side-chains 169 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 447 LYS Chi-restraints excluded: chain L residue 799 VAL Chi-restraints excluded: chain L residue 1254 SER Chi-restraints excluded: chain L residue 1307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 870 ASN L1035 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.208641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.172154 restraints weight = 19912.161| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.61 r_work: 0.3813 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12496 Z= 0.125 Angle : 0.573 10.623 16892 Z= 0.294 Chirality : 0.041 0.148 1923 Planarity : 0.004 0.052 2139 Dihedral : 4.265 45.221 1681 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.03 % Allowed : 20.31 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1515 helix: 2.41 (0.18), residues: 825 sheet: 0.79 (0.55), residues: 102 loop : -0.45 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L1150 TYR 0.021 0.001 TYR L1310 PHE 0.021 0.002 PHE L 392 TRP 0.015 0.001 TRP L1189 HIS 0.006 0.001 HIS L 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12487) covalent geometry : angle 0.57086 / 0.29 (16890) hydrogen bonds : bond 0.04596 / 3.04 ( 666) hydrogen bonds : angle 3.72085 / 2.70 ( 1888) metal coordination : bond 0.01398 / 0.54 ( 9) metal coordination : angle 4.01918 / 2.21 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5296.14 seconds wall clock time: 90 minutes 41.62 seconds (5441.62 seconds total)