Starting phenix.real_space_refine on Thu Aug 6 00:10:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.map" model { file = "/net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vuk_65366/08_2026/9vuk_65366.cif" } resolution = 3.17 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= 0.035 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 2 6.06 5 S 63 5.16 5 C 7731 2.51 5 N 2090 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s 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: 12116 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 3 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: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain breaks: 1 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: 10133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1262, 10121 Classifications: {'peptide': 1262} Link IDs: {'PTRANS': 53, 'TRANS': 1208} Unresolved chain links: 1 Chain breaks: 5 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: 1262, 10121 Classifications: {'peptide': 1262} Link IDs: {'PTRANS': 53, 'TRANS': 1208} Unresolved chain links: 1 Chain breaks: 5 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: 10332 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10719 SG CYS L1177 19.974 72.487 114.856 1.00104.93 S ATOM 10740 SG CYS L1180 20.644 76.259 114.446 1.00110.60 S ATOM 10353 SG CYS L1132 41.301 74.367 121.549 1.00 91.29 S ATOM 11863 SG CYS L1369 38.237 75.792 122.321 1.00119.68 S ATOM 11869 SG CYS L1370 40.288 75.188 119.145 1.00 91.88 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR L1333 " occ=0.57 ... (22 atoms not shown) pdb=" OH BTYR L1333 " occ=0.43 Time building chain proxies: 3.80, per 1000 atoms: 0.31 Number of scatterers: 12116 At special positions: 0 Unit cell: (93.93, 109.74, 145.08, 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 2 29.99 S 63 16.00 O 2230 8.00 N 2090 7.00 C 7731 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: 0.77 Conformation dependent library (CDL) restraints added in 838.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L4001 " pdb="ZN ZN L4001 " - pdb=" NE2 HIS L1364 " pdb="ZN ZN L4001 " - pdb=" ND1 HIS L1362 " pdb="ZN ZN L4001 " - pdb=" SG CYS L1177 " pdb="ZN ZN L4001 " - pdb=" SG CYS L1180 " pdb=" ZN L4002 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1132 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1370 " pdb="ZN ZN L4002 " - pdb=" SG CYS L1369 " Number of angles added : 1 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 62.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 341 through 369 removed outlier: 3.695A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.471A pdb=" N GLU A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.670A pdb=" N ARG A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.711A pdb=" N ASP A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 506 removed outlier: 4.052A pdb=" N MET A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 371 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 399 removed outlier: 3.508A pdb=" N ILE C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 369 removed outlier: 3.761A pdb=" N SER D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 33 Processing helix chain 'L' and resid 43 through 56 Processing helix chain 'L' and resid 59 through 77 removed outlier: 3.625A pdb=" N ARG L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) 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 135 removed outlier: 3.714A pdb=" N VAL L 120 " --> pdb=" O LEU L 116 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASP L 122 " --> pdb=" O SER L 118 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 151 removed outlier: 3.520A 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 225 through 248 Processing helix chain 'L' and resid 251 through 273 removed outlier: 3.803A pdb=" N GLY L 256 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY L 267 " --> pdb=" O LYS L 263 " (cutoff:3.500A) Proline residue: L 270 - end of helix Processing helix chain 'L' and resid 275 through 282 removed outlier: 3.848A pdb=" N ILE L 279 " --> pdb=" O PRO L 275 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 292 removed outlier: 3.991A pdb=" N LEU L 288 " --> pdb=" O GLU L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 295 No H-bonds generated for 'chain 'L' and resid 293 through 295' Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 302 through 320 removed outlier: 4.094A pdb=" N HIS L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN L 319 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY L 320 " --> pdb=" O LEU L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 339 removed outlier: 3.526A pdb=" N TYR L 327 " --> pdb=" O ASP L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 344 No H-bonds generated for 'chain 'L' and resid 342 through 344' Processing helix chain 'L' and resid 345 through 351 removed outlier: 3.524A pdb=" N ILE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE L 350 " --> pdb=" O THR L 346 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER L 351 " --> pdb=" O GLY L 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 345 through 351' Processing helix chain 'L' and resid 352 through 355 Processing helix chain 'L' and resid 362 through 375 removed outlier: 3.657A pdb=" N ALA L 366 " --> pdb=" O GLU L 362 " (cutoff:3.500A) removed outlier: 3.605A 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 removed outlier: 3.630A pdb=" N ALA L 444 " --> pdb=" O LYS L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 removed outlier: 3.799A pdb=" N LEU L 464 " --> pdb=" O LEU L 460 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS L 465 " --> pdb=" O THR L 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 460 through 465' Processing helix chain 'L' and resid 472 through 480 removed outlier: 5.679A pdb=" N ASP L 477 " --> pdb=" O ARG L 474 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL L 479 " --> pdb=" O TRP L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 485 Processing helix chain 'L' and resid 497 through 504 Processing helix chain 'L' and resid 509 through 519 removed outlier: 3.971A pdb=" N VAL L 517 " --> pdb=" O VAL L 513 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 567 removed outlier: 3.797A pdb=" N GLY L 567 " --> pdb=" O LEU L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 570 through 574 removed outlier: 3.914A pdb=" N ASP L 574 " --> pdb=" O TYR L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 670 Processing helix chain 'L' and resid 672 through 688 removed outlier: 4.773A pdb=" N LEU L 678 " --> pdb=" O GLU L 674 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE L 679 " --> pdb=" O THR L 675 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 701 Processing helix chain 'L' and resid 721 through 725 removed outlier: 3.531A pdb=" N VAL L 725 " --> pdb=" O LEU L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 743 through 762 Proline residue: L 753 - end of helix Processing helix chain 'L' and resid 788 through 814 Processing helix chain 'L' and resid 845 through 851 removed outlier: 4.454A pdb=" N SER L 849 " --> pdb=" O GLN L 845 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE L 850 " --> pdb=" O SER L 846 " (cutoff:3.500A) Processing helix chain 'L' and resid 863 through 881 Processing helix chain 'L' and resid 884 through 906 Processing helix chain 'L' and resid 913 through 922 Proline residue: L 919 - end of helix Processing helix chain 'L' and resid 924 through 933 Processing helix chain 'L' and resid 945 through 949 Processing helix chain 'L' and resid 955 through 970 Processing helix chain 'L' and resid 974 through 983 removed outlier: 4.213A pdb=" N LEU L 978 " --> pdb=" O PRO L 974 " (cutoff:3.500A) removed outlier: 3.841A 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 Processing helix chain 'L' and resid 1027 through 1031 Processing helix chain 'L' and resid 1037 through 1051 Processing helix chain 'L' and resid 1056 through 1067 Processing helix chain 'L' and resid 1067 through 1079 Processing helix chain 'L' and resid 1082 through 1093 Processing helix chain 'L' and resid 1096 through 1105 Processing helix chain 'L' and resid 1105 through 1119 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 1182 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 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: 3.696A pdb=" N ILE A 372 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA D 373 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 6.638A 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: 6.505A 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: 6.354A pdb=" N SER L 83 " --> pdb=" O VAL L 220 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR L 222 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS L 219 " --> pdb=" O SER L 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 411 through 412 removed outlier: 3.636A pdb=" N LYS L 447 " --> pdb=" O THR L 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 530 through 534 Processing sheet with id=AA6, first strand: chain 'L' and resid 765 through 771 removed outlier: 3.543A pdb=" N ARG L 765 " --> pdb=" O THR L 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 704 through 706 Processing sheet with id=AA8, first strand: chain 'L' and resid 830 through 832 Processing sheet with id=AA9, first strand: chain 'L' and resid 1166 through 1171 672 hydrogen bonds defined for protein. 1936 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: 2.07 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1964 1.29 - 1.42: 3128 1.42 - 1.55: 7151 1.55 - 1.68: 8 1.68 - 1.81: 103 Bond restraints: 12354 Sorted by residual: bond pdb=" N ASN L 924 " pdb=" CA ASN L 924 " ideal model delta sigma weight residual 1.458 1.551 -0.093 1.30e-02 5.92e+03 5.16e+01 bond pdb=" CA ASN L 923 " pdb=" C ASN L 923 " ideal model delta sigma weight residual 1.520 1.588 -0.068 1.20e-02 6.94e+03 3.18e+01 bond pdb=" CB ASN L 923 " pdb=" CG ASN L 923 " ideal model delta sigma weight residual 1.516 1.414 0.102 2.50e-02 1.60e+03 1.68e+01 bond pdb=" CG ASN L 923 " pdb=" OD1 ASN L 923 " ideal model delta sigma weight residual 1.231 1.156 0.075 1.90e-02 2.77e+03 1.56e+01 bond pdb=" CG LYS L 724 " pdb=" CD LYS L 724 " ideal model delta sigma weight residual 1.520 1.407 0.113 3.00e-02 1.11e+03 1.42e+01 ... (remaining 12349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.84: 16700 11.84 - 23.67: 6 23.67 - 35.51: 2 35.51 - 47.35: 0 47.35 - 59.18: 1 Bond angle restraints: 16709 Sorted by residual: angle pdb=" CB ASN L 923 " pdb=" CG ASN L 923 " pdb=" OD1 ASN L 923 " ideal model delta sigma weight residual 120.80 179.98 -59.18 2.00e+00 2.50e-01 8.76e+02 angle pdb=" OD1 ASN L 923 " pdb=" CG ASN L 923 " pdb=" ND2 ASN L 923 " ideal model delta sigma weight residual 122.60 96.89 25.71 1.00e+00 1.00e+00 6.61e+02 angle pdb=" CB ASN L 923 " pdb=" CG ASN L 923 " pdb=" ND2 ASN L 923 " ideal model delta sigma weight residual 116.40 83.13 33.27 1.50e+00 4.44e-01 4.92e+02 angle pdb=" N ASN L 923 " pdb=" CA ASN L 923 " pdb=" C ASN L 923 " ideal model delta sigma weight residual 108.48 86.52 21.96 1.80e+00 3.09e-01 1.49e+02 angle pdb=" C THR L 922 " pdb=" N ASN L 923 " pdb=" CA ASN L 923 " ideal model delta sigma weight residual 121.89 107.81 14.08 1.74e+00 3.30e-01 6.55e+01 ... (remaining 16704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6558 17.74 - 35.49: 757 35.49 - 53.23: 154 53.23 - 70.98: 21 70.98 - 88.72: 6 Dihedral angle restraints: 7496 sinusoidal: 3058 harmonic: 4438 Sorted by residual: dihedral pdb=" CA THR L 922 " pdb=" C THR L 922 " pdb=" N ASN L 923 " pdb=" CA ASN L 923 " ideal model delta harmonic sigma weight residual -180.00 -151.71 -28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" C ASN L 923 " pdb=" N ASN L 923 " pdb=" CA ASN L 923 " pdb=" CB ASN L 923 " ideal model delta harmonic sigma weight residual -122.60 -110.50 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" CA ASP L 728 " pdb=" C ASP L 728 " pdb=" N GLN L 729 " pdb=" CA GLN L 729 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1860 0.105 - 0.211: 45 0.211 - 0.316: 1 0.316 - 0.422: 0 0.422 - 0.527: 1 Chirality restraints: 1907 Sorted by residual: chirality pdb=" CA ASN L 923 " pdb=" N ASN L 923 " pdb=" C ASN L 923 " pdb=" CB ASN L 923 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.95e+00 chirality pdb=" CA THR L 922 " pdb=" N THR L 922 " pdb=" C THR L 922 " pdb=" CB THR L 922 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN L 924 " pdb=" N ASN L 924 " pdb=" C ASN L 924 " pdb=" CB ASN L 924 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1904 not shown) Planarity restraints: 2113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 463 " 0.043 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR L 463 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR L 463 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 463 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR L 463 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR L 463 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR L 463 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR L 463 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 922 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C THR L 922 " 0.066 2.00e-02 2.50e+03 pdb=" O THR L 922 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN L 923 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 923 " -0.020 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ASN L 923 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN L 923 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN L 924 " -0.022 2.00e-02 2.50e+03 ... (remaining 2110 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 59 2.46 - 3.07: 8257 3.07 - 3.68: 18732 3.68 - 4.29: 27187 4.29 - 4.90: 45191 Nonbonded interactions: 99426 Sorted by model distance: nonbonded pdb=" OH TYR L1155 " pdb=" O PRO L1373 " model vdw 1.847 3.040 nonbonded pdb=" OD1 ASN L 132 " pdb=" OH TYR L 886 " model vdw 1.975 3.040 nonbonded pdb=" OD1 ASP L 317 " pdb=" OG SER L 322 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP L 122 " pdb=" NZ LYS L 123 " model vdw 2.152 3.120 nonbonded pdb=" OG1 THR L 859 " pdb=" O VAL L 861 " model vdw 2.155 3.040 ... (remaining 99421 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.280 Find NCS groups from input model: 0.070 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.005 0.113 12361 Z= 0.232 Angle : 0.937 59.183 16710 Z= 0.531 Chirality : 0.045 0.527 1907 Planarity : 0.005 0.049 2113 Dihedral : 15.286 88.723 4626 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.19 % Allowed : 17.85 % Favored : 80.96 % 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: 1.19 (0.22), residues: 1493 helix: 1.59 (0.18), residues: 828 sheet: 0.24 (0.56), residues: 97 loop : -0.23 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 33 TYR 0.050 0.003 TYR L 723 PHE 0.033 0.002 PHE L 546 TRP 0.018 0.002 TRP L 440 HIS 0.008 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (12354) covalent geometry : angle 0.93709 / 0.53 (16709) hydrogen bonds : bond 0.14290 / 9.73 ( 672) hydrogen bonds : angle 5.34791 / 3.88 ( 1936) metal coordination : bond 0.00483 / 0.28 ( 7) metal coordination : angle 3.20566 / 1.69 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.6078 (mtp) cc_final: 0.5855 (tmm) REVERT: A 506 MET cc_start: 0.7293 (mpp) cc_final: 0.6899 (mtm) REVERT: C 371 MET cc_start: 0.7123 (tpp) cc_final: 0.6661 (mmm) REVERT: D 371 MET cc_start: 0.6018 (mmt) cc_final: 0.5612 (mmt) REVERT: L 61 MET cc_start: 0.6139 (mpp) cc_final: 0.5840 (mmt) REVERT: L 147 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7119 (mm-30) REVERT: L 175 MET cc_start: 0.8290 (ttm) cc_final: 0.8070 (ttt) REVERT: L 263 LYS cc_start: 0.8041 (tttm) cc_final: 0.7806 (ttpp) REVERT: L 277 TYR cc_start: 0.8019 (m-80) cc_final: 0.7476 (m-80) REVERT: L 306 ASN cc_start: 0.8382 (t0) cc_final: 0.8170 (t0) REVERT: L 380 ILE cc_start: 0.8400 (pt) cc_final: 0.7950 (tt) REVERT: L 702 THR cc_start: 0.8339 (p) cc_final: 0.7923 (t) REVERT: L 819 LYS cc_start: 0.6474 (mttm) cc_final: 0.6250 (mtpp) REVERT: L 845 GLN cc_start: 0.6654 (tt0) cc_final: 0.6050 (pt0) REVERT: L 863 GLU cc_start: 0.7760 (pm20) cc_final: 0.7097 (tt0) REVERT: L 1016 ILE cc_start: 0.7496 (mm) cc_final: 0.7201 (mp) REVERT: L 1083 LYS cc_start: 0.5714 (mttt) cc_final: 0.5486 (mmtm) REVERT: L 1144 MET cc_start: 0.8303 (tpp) cc_final: 0.8093 (mmm) REVERT: L 1380 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6645 (mp) outliers start: 16 outliers final: 7 residues processed: 279 average time/residue: 0.1072 time to fit residues: 42.3372 Evaluate side-chains 216 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 923 ASN Chi-restraints excluded: chain L residue 977 THR Chi-restraints excluded: chain L residue 1035 HIS Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN L 557 GLN ** L 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1053 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.221872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186416 restraints weight = 17467.972| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.16 r_work: 0.3845 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12361 Z= 0.140 Angle : 0.601 12.486 16710 Z= 0.307 Chirality : 0.042 0.154 1907 Planarity : 0.005 0.067 2113 Dihedral : 4.747 59.772 1672 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.52 % Allowed : 16.44 % Favored : 81.04 % 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: 1.39 (0.22), residues: 1493 helix: 1.83 (0.18), residues: 838 sheet: 0.17 (0.54), residues: 94 loop : -0.28 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L1233 TYR 0.024 0.002 TYR L 327 PHE 0.029 0.002 PHE L 546 TRP 0.016 0.002 TRP L 440 HIS 0.005 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12354) covalent geometry : angle 0.60062 / 0.31 (16709) hydrogen bonds : bond 0.03653 / 2.39 ( 672) hydrogen bonds : angle 4.17859 / 3.02 ( 1936) metal coordination : bond 0.00656 / 0.42 ( 7) metal coordination : angle 2.43386 / 1.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.6416 (mtp) cc_final: 0.6161 (tmm) REVERT: C 371 MET cc_start: 0.7281 (tpp) cc_final: 0.6787 (mtm) REVERT: D 371 MET cc_start: 0.6640 (mmt) cc_final: 0.6264 (mmt) REVERT: L 231 TYR cc_start: 0.8775 (m-80) cc_final: 0.8445 (m-80) REVERT: L 277 TYR cc_start: 0.7841 (m-80) cc_final: 0.7319 (m-80) REVERT: L 386 MET cc_start: 0.7663 (mmm) cc_final: 0.7426 (mmm) REVERT: L 548 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: L 691 SER cc_start: 0.8246 (t) cc_final: 0.7811 (m) REVERT: L 702 THR cc_start: 0.8314 (p) cc_final: 0.8026 (t) REVERT: L 716 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6951 (mt) REVERT: L 838 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: L 883 TYR cc_start: 0.8269 (t80) cc_final: 0.7899 (t80) REVERT: L 912 MET cc_start: 0.7774 (mmt) cc_final: 0.7349 (mmt) REVERT: L 967 MET cc_start: 0.6734 (mtt) cc_final: 0.6458 (mtt) REVERT: L 1012 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7535 (mt) REVERT: L 1016 ILE cc_start: 0.7720 (mm) cc_final: 0.7387 (mp) REVERT: L 1063 ILE cc_start: 0.8476 (mp) cc_final: 0.8243 (mp) REVERT: L 1083 LYS cc_start: 0.5876 (mttt) cc_final: 0.5539 (mmtm) REVERT: L 1121 ARG cc_start: 0.7339 (mmm160) cc_final: 0.6883 (mmm160) REVERT: L 1380 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6496 (mp) outliers start: 34 outliers final: 17 residues processed: 237 average time/residue: 0.1004 time to fit residues: 33.7880 Evaluate side-chains 209 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 513 VAL Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 716 LEU Chi-restraints excluded: chain L residue 780 THR Chi-restraints excluded: chain L residue 826 SER Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 841 LEU Chi-restraints excluded: chain L residue 842 LEU Chi-restraints excluded: chain L residue 861 VAL Chi-restraints excluded: chain L residue 928 ILE Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1012 LEU Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN L 404 HIS L 729 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.210671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167476 restraints weight = 22876.370| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 3.85 r_work: 0.3726 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 12361 Z= 0.246 Angle : 0.687 10.260 16710 Z= 0.352 Chirality : 0.046 0.255 1907 Planarity : 0.005 0.042 2113 Dihedral : 4.793 40.634 1664 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.85 % Allowed : 15.85 % Favored : 80.30 % 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: 0.93 (0.22), residues: 1493 helix: 1.41 (0.18), residues: 841 sheet: -0.27 (0.54), residues: 97 loop : -0.36 (0.27), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L1233 TYR 0.026 0.003 TYR L 551 PHE 0.031 0.003 PHE L 572 TRP 0.015 0.002 TRP L 787 HIS 0.009 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (12354) covalent geometry : angle 0.68722 / 0.35 (16709) hydrogen bonds : bond 0.04225 / 2.76 ( 672) hydrogen bonds : angle 4.41073 / 3.18 ( 1936) metal coordination : bond 0.00209 / 0.10 ( 7) metal coordination : angle 0.07564 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.259 Fit side-chains REVERT: A 371 MET cc_start: 0.6777 (mtp) cc_final: 0.6122 (tmm) REVERT: B 342 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5350 (tt) REVERT: C 371 MET cc_start: 0.7298 (tpp) cc_final: 0.6781 (mtm) REVERT: D 371 MET cc_start: 0.7119 (mmt) cc_final: 0.6835 (mmt) REVERT: L 61 MET cc_start: 0.6869 (mpp) cc_final: 0.5738 (ttt) REVERT: L 104 ARG cc_start: 0.7347 (ttp-110) cc_final: 0.6924 (ttm110) REVERT: L 362 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7919 (mt-10) REVERT: L 368 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6797 (mm-30) REVERT: L 548 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8196 (mtmt) REVERT: L 702 THR cc_start: 0.8760 (p) cc_final: 0.8536 (t) REVERT: L 716 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7652 (mt) REVERT: L 721 PRO cc_start: 0.8155 (Cg_exo) cc_final: 0.7909 (Cg_endo) REVERT: L 794 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6677 (mmt90) REVERT: L 838 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: L 858 GLU cc_start: 0.7098 (pm20) cc_final: 0.6743 (mp0) REVERT: L 963 ASP cc_start: 0.7645 (t0) cc_final: 0.7413 (t0) REVERT: L 967 MET cc_start: 0.7653 (mtt) cc_final: 0.7307 (mtt) REVERT: L 1112 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: L 1199 ASP cc_start: 0.7413 (t70) cc_final: 0.7175 (t70) REVERT: L 1380 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6755 (mp) outliers start: 52 outliers final: 26 residues processed: 240 average time/residue: 0.1092 time to fit residues: 36.4425 Evaluate side-chains 216 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 513 VAL Chi-restraints excluded: chain L residue 522 TYR Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 669 LEU Chi-restraints excluded: chain L residue 703 SER Chi-restraints excluded: chain L residue 716 LEU Chi-restraints excluded: chain L residue 780 THR Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 842 LEU Chi-restraints excluded: chain L residue 850 ILE Chi-restraints excluded: chain L residue 861 VAL Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 918 ILE Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1102 ARG Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 GLN ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN L 729 GLN L1053 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.214096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171144 restraints weight = 22780.426| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.53 r_work: 0.3778 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12361 Z= 0.139 Angle : 0.574 11.499 16710 Z= 0.291 Chirality : 0.041 0.140 1907 Planarity : 0.004 0.034 2113 Dihedral : 4.492 43.618 1664 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.44 % Allowed : 17.26 % Favored : 80.30 % 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: 1.16 (0.22), residues: 1493 helix: 1.61 (0.18), residues: 850 sheet: -0.45 (0.53), residues: 99 loop : -0.25 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 465 TYR 0.017 0.002 TYR L 31 PHE 0.023 0.002 PHE L1191 TRP 0.013 0.001 TRP L1189 HIS 0.005 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12354) covalent geometry : angle 0.57418 / 0.29 (16709) hydrogen bonds : bond 0.03448 / 2.27 ( 672) hydrogen bonds : angle 4.12157 / 2.99 ( 1936) metal coordination : bond 0.00290 / 0.19 ( 7) metal coordination : angle 2.52497 / 1.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.399 Fit side-chains REVERT: A 371 MET cc_start: 0.6702 (mtp) cc_final: 0.6131 (mtm) REVERT: C 371 MET cc_start: 0.7320 (tpp) cc_final: 0.6842 (mtm) REVERT: D 371 MET cc_start: 0.6939 (mmt) cc_final: 0.6684 (mmt) REVERT: L 61 MET cc_start: 0.6812 (mpp) cc_final: 0.5762 (ttt) REVERT: L 104 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.6901 (ttm110) REVERT: L 231 TYR cc_start: 0.8939 (m-80) cc_final: 0.8612 (m-80) REVERT: L 277 TYR cc_start: 0.8062 (m-80) cc_final: 0.7544 (m-80) REVERT: L 368 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6673 (mm-30) REVERT: L 548 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: L 654 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: L 702 THR cc_start: 0.8650 (p) cc_final: 0.8449 (t) REVERT: L 716 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7746 (mt) REVERT: L 721 PRO cc_start: 0.8230 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: L 794 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6646 (mmt90) REVERT: L 838 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: L 967 MET cc_start: 0.7524 (mtt) cc_final: 0.7226 (mtt) REVERT: L 1108 TYR cc_start: 0.7192 (t80) cc_final: 0.6813 (t80) REVERT: L 1112 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: L 1398 ILE cc_start: 0.8484 (mm) cc_final: 0.8030 (pt) outliers start: 33 outliers final: 19 residues processed: 215 average time/residue: 0.1078 time to fit residues: 32.6084 Evaluate side-chains 197 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 654 GLU Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 716 LEU Chi-restraints excluded: chain L residue 780 THR Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 842 LEU Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 0.0010 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 366 HIS ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 HIS L 562 ASN L1053 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.215712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173205 restraints weight = 22994.999| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.56 r_work: 0.3797 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12361 Z= 0.122 Angle : 0.553 10.000 16710 Z= 0.277 Chirality : 0.039 0.156 1907 Planarity : 0.004 0.037 2113 Dihedral : 4.330 43.233 1664 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.30 % Allowed : 17.78 % Favored : 79.93 % 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: 1.37 (0.22), residues: 1493 helix: 1.81 (0.18), residues: 851 sheet: -0.31 (0.53), residues: 99 loop : -0.23 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L1233 TYR 0.013 0.001 TYR L 837 PHE 0.015 0.001 PHE L 546 TRP 0.013 0.001 TRP L1189 HIS 0.004 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (12354) covalent geometry : angle 0.55266 / 0.28 (16709) hydrogen bonds : bond 0.03184 / 2.09 ( 672) hydrogen bonds : angle 3.97692 / 2.88 ( 1936) metal coordination : bond 0.00254 / 0.16 ( 7) metal coordination : angle 2.37320 / 1.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6495 (mtp) cc_final: 0.5837 (mtm) REVERT: C 371 MET cc_start: 0.7336 (tpp) cc_final: 0.6869 (mtm) REVERT: D 371 MET cc_start: 0.6864 (mmt) cc_final: 0.6626 (mmt) REVERT: L 61 MET cc_start: 0.6602 (mpp) cc_final: 0.6273 (mmp) REVERT: L 104 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6874 (ttm110) REVERT: L 277 TYR cc_start: 0.8035 (m-80) cc_final: 0.7430 (m-80) REVERT: L 368 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6705 (mm-30) REVERT: L 548 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7997 (mtmt) REVERT: L 654 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: L 702 THR cc_start: 0.8693 (p) cc_final: 0.8474 (t) REVERT: L 721 PRO cc_start: 0.8248 (Cg_exo) cc_final: 0.7965 (Cg_endo) REVERT: L 838 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: L 967 MET cc_start: 0.7434 (mtt) cc_final: 0.7117 (mtt) REVERT: L 973 MET cc_start: 0.8217 (mtt) cc_final: 0.7887 (mtt) REVERT: L 1054 ILE cc_start: 0.8309 (tt) cc_final: 0.7970 (pt) REVERT: L 1380 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.6941 (mp) REVERT: L 1398 ILE cc_start: 0.8419 (mm) cc_final: 0.8024 (pt) REVERT: L 1399 TYR cc_start: 0.7846 (t80) cc_final: 0.7580 (t80) outliers start: 31 outliers final: 20 residues processed: 200 average time/residue: 0.1021 time to fit residues: 28.4078 Evaluate side-chains 194 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 654 GLU Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 780 THR Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 850 ILE Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1347 LEU Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 711 HIS L1315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.217504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.175126 restraints weight = 21650.278| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.55 r_work: 0.3822 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12361 Z= 0.109 Angle : 0.545 10.589 16710 Z= 0.271 Chirality : 0.039 0.142 1907 Planarity : 0.004 0.044 2113 Dihedral : 4.191 42.642 1664 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.70 % Allowed : 18.81 % Favored : 79.48 % 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: 1.50 (0.22), residues: 1493 helix: 1.94 (0.18), residues: 855 sheet: -0.17 (0.53), residues: 98 loop : -0.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L1233 TYR 0.020 0.001 TYR L 723 PHE 0.021 0.001 PHE L1191 TRP 0.014 0.001 TRP L1189 HIS 0.004 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (12354) covalent geometry : angle 0.54453 / 0.27 (16709) hydrogen bonds : bond 0.03035 / 2.00 ( 672) hydrogen bonds : angle 3.89942 / 2.84 ( 1936) metal coordination : bond 0.00332 / 0.21 ( 7) metal coordination : angle 2.62733 / 1.38 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6595 (mtp) cc_final: 0.5969 (mtm) REVERT: C 371 MET cc_start: 0.7399 (tpp) cc_final: 0.6896 (mtm) REVERT: D 371 MET cc_start: 0.6681 (mmt) cc_final: 0.6360 (mmt) REVERT: L 104 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.6848 (ttm110) REVERT: L 230 MET cc_start: 0.8724 (ttp) cc_final: 0.8501 (ttp) REVERT: L 277 TYR cc_start: 0.7986 (m-80) cc_final: 0.7352 (m-80) REVERT: L 368 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6700 (mm-30) REVERT: L 535 LYS cc_start: 0.7532 (tptp) cc_final: 0.7290 (tmtt) REVERT: L 548 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8063 (mtmt) REVERT: L 702 THR cc_start: 0.8651 (p) cc_final: 0.8439 (t) REVERT: L 721 PRO cc_start: 0.8235 (Cg_exo) cc_final: 0.7954 (Cg_endo) REVERT: L 838 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: L 967 MET cc_start: 0.7421 (mtt) cc_final: 0.7138 (mtt) REVERT: L 973 MET cc_start: 0.8164 (mtt) cc_final: 0.7879 (mtt) REVERT: L 1016 ILE cc_start: 0.7875 (mm) cc_final: 0.7616 (mt) REVERT: L 1054 ILE cc_start: 0.8282 (tt) cc_final: 0.7956 (pt) REVERT: L 1380 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.6901 (mp) REVERT: L 1397 LEU cc_start: 0.8193 (tt) cc_final: 0.7736 (tp) REVERT: L 1398 ILE cc_start: 0.8430 (mm) cc_final: 0.8122 (pt) REVERT: L 1399 TYR cc_start: 0.7682 (t80) cc_final: 0.7403 (t80) outliers start: 23 outliers final: 14 residues processed: 196 average time/residue: 0.0995 time to fit residues: 27.5398 Evaluate side-chains 181 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.0570 chunk 128 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN L 435 GLN ** L1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.217124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.174206 restraints weight = 25113.601| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 4.03 r_work: 0.3789 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 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 = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12361 Z= 0.111 Angle : 0.538 8.969 16710 Z= 0.268 Chirality : 0.039 0.142 1907 Planarity : 0.004 0.044 2113 Dihedral : 4.055 30.045 1664 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.78 % Allowed : 18.96 % Favored : 79.26 % 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: 1.58 (0.22), residues: 1493 helix: 2.02 (0.18), residues: 854 sheet: -0.19 (0.54), residues: 99 loop : -0.26 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L1233 TYR 0.013 0.001 TYR L 571 PHE 0.015 0.001 PHE L 546 TRP 0.013 0.001 TRP L1189 HIS 0.004 0.001 HIS L1364 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (12354) covalent geometry : angle 0.53821 / 0.27 (16709) hydrogen bonds : bond 0.03000 / 1.97 ( 672) hydrogen bonds : angle 3.84939 / 2.79 ( 1936) metal coordination : bond 0.00283 / 0.18 ( 7) metal coordination : angle 2.26032 / 1.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6628 (mtp) cc_final: 0.6031 (mtm) REVERT: C 371 MET cc_start: 0.7418 (tpp) cc_final: 0.6903 (mtm) REVERT: D 371 MET cc_start: 0.6683 (mmt) cc_final: 0.6361 (mmt) REVERT: L 61 MET cc_start: 0.6517 (mpp) cc_final: 0.5617 (ttp) REVERT: L 104 ARG cc_start: 0.7354 (ttp-110) cc_final: 0.6854 (ttm110) REVERT: L 277 TYR cc_start: 0.8006 (m-80) cc_final: 0.7349 (m-80) REVERT: L 368 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6747 (mm-30) REVERT: L 535 LYS cc_start: 0.7501 (tptp) cc_final: 0.7280 (tmtt) REVERT: L 548 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8006 (mtmt) REVERT: L 654 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: L 702 THR cc_start: 0.8670 (p) cc_final: 0.8453 (t) REVERT: L 721 PRO cc_start: 0.8256 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: L 838 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: L 967 MET cc_start: 0.7428 (mtt) cc_final: 0.7130 (mtt) REVERT: L 973 MET cc_start: 0.8258 (mtt) cc_final: 0.8043 (mtt) REVERT: L 1016 ILE cc_start: 0.7841 (mm) cc_final: 0.7581 (mt) REVERT: L 1380 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 24 outliers final: 17 residues processed: 186 average time/residue: 0.0927 time to fit residues: 24.6701 Evaluate side-chains 188 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 371 ARG Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 654 GLU Chi-restraints excluded: chain L residue 655 THR Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 940 MET Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN ** L 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 435 GLN ** L1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.213622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171251 restraints weight = 22838.311| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.73 r_work: 0.3716 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12361 Z= 0.134 Angle : 0.555 8.063 16710 Z= 0.278 Chirality : 0.040 0.144 1907 Planarity : 0.004 0.049 2113 Dihedral : 4.076 29.162 1664 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.70 % Allowed : 18.81 % Favored : 79.48 % 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: 1.51 (0.22), residues: 1493 helix: 1.92 (0.18), residues: 855 sheet: -0.17 (0.52), residues: 101 loop : -0.21 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 465 TYR 0.020 0.002 TYR L 382 PHE 0.038 0.002 PHE L 502 TRP 0.025 0.001 TRP L1189 HIS 0.005 0.001 HIS L 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (12354) covalent geometry : angle 0.55458 / 0.28 (16709) hydrogen bonds : bond 0.03159 / 2.07 ( 672) hydrogen bonds : angle 3.90510 / 2.83 ( 1936) metal coordination : bond 0.00114 / 0.06 ( 7) metal coordination : angle 1.57708 / 0.83 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6614 (mtp) cc_final: 0.6005 (mtm) REVERT: C 371 MET cc_start: 0.7464 (tpp) cc_final: 0.6894 (mtm) REVERT: D 371 MET cc_start: 0.6858 (mmt) cc_final: 0.6556 (mmt) REVERT: L 368 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6831 (mm-30) REVERT: L 535 LYS cc_start: 0.7611 (tptp) cc_final: 0.7398 (tmtt) REVERT: L 548 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (mtmt) REVERT: L 654 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: L 838 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: L 967 MET cc_start: 0.7531 (mtt) cc_final: 0.7247 (mtt) REVERT: L 973 MET cc_start: 0.8311 (mtt) cc_final: 0.8056 (mtt) REVERT: L 1380 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.6921 (mp) outliers start: 23 outliers final: 15 residues processed: 181 average time/residue: 0.1104 time to fit residues: 27.7898 Evaluate side-chains 179 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 654 GLU Chi-restraints excluded: chain L residue 838 TYR Chi-restraints excluded: chain L residue 842 LEU Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 HIS ** L 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.215788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173703 restraints weight = 21535.900| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 3.58 r_work: 0.3749 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12361 Z= 0.116 Angle : 0.549 8.750 16710 Z= 0.273 Chirality : 0.039 0.139 1907 Planarity : 0.004 0.047 2113 Dihedral : 3.999 27.153 1663 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.56 % Allowed : 19.19 % Favored : 79.26 % 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: 1.56 (0.22), residues: 1493 helix: 1.98 (0.18), residues: 854 sheet: -0.06 (0.53), residues: 100 loop : -0.23 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 465 TYR 0.020 0.001 TYR L 31 PHE 0.018 0.002 PHE L1191 TRP 0.026 0.001 TRP L1189 HIS 0.004 0.001 HIS L1364 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12354) covalent geometry : angle 0.54859 / 0.27 (16709) hydrogen bonds : bond 0.03009 / 1.97 ( 672) hydrogen bonds : angle 3.83870 / 2.77 ( 1936) metal coordination : bond 0.00249 / 0.15 ( 7) metal coordination : angle 2.29130 / 1.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6608 (mtp) cc_final: 0.6006 (mtm) REVERT: C 371 MET cc_start: 0.7468 (tpp) cc_final: 0.6925 (mtm) REVERT: D 371 MET cc_start: 0.6833 (mmt) cc_final: 0.6550 (mmt) REVERT: L 61 MET cc_start: 0.6530 (mpp) cc_final: 0.5928 (mmm) REVERT: L 368 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6854 (mm-30) REVERT: L 548 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7986 (mtmt) REVERT: L 967 MET cc_start: 0.7426 (mtt) cc_final: 0.7109 (mtt) REVERT: L 973 MET cc_start: 0.8217 (mtt) cc_final: 0.7989 (mtt) REVERT: L 985 GLN cc_start: 0.8450 (tt0) cc_final: 0.8168 (tp40) REVERT: L 1016 ILE cc_start: 0.7959 (mm) cc_final: 0.7700 (mt) REVERT: L 1054 ILE cc_start: 0.8295 (tt) cc_final: 0.8062 (pt) REVERT: L 1380 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6883 (mp) outliers start: 21 outliers final: 14 residues processed: 182 average time/residue: 0.0989 time to fit residues: 25.6900 Evaluate side-chains 175 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 981 VAL Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 16 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 GLN ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 306 ASN ** L 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN ** L1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157661 restraints weight = 21990.261| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.21 r_work: 0.3465 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12361 Z= 0.142 Angle : 0.565 8.919 16710 Z= 0.282 Chirality : 0.040 0.146 1907 Planarity : 0.004 0.064 2113 Dihedral : 4.058 28.987 1663 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.41 % Allowed : 19.63 % Favored : 78.96 % 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: 1.42 (0.22), residues: 1493 helix: 1.83 (0.18), residues: 856 sheet: -0.21 (0.52), residues: 101 loop : -0.21 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 465 TYR 0.021 0.002 TYR L 31 PHE 0.018 0.002 PHE L1191 TRP 0.025 0.001 TRP L1189 HIS 0.005 0.001 HIS L 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (12354) covalent geometry : angle 0.56445 / 0.28 (16709) hydrogen bonds : bond 0.03175 / 2.08 ( 672) hydrogen bonds : angle 3.90784 / 2.82 ( 1936) metal coordination : bond 0.00209 / 0.12 ( 7) metal coordination : angle 1.24303 / 0.65 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 371 MET cc_start: 0.6644 (mtp) cc_final: 0.6067 (mtm) REVERT: A 465 ARG cc_start: 0.7118 (mtp85) cc_final: 0.6868 (mtp85) REVERT: C 371 MET cc_start: 0.7457 (tpp) cc_final: 0.6844 (mtm) REVERT: D 371 MET cc_start: 0.7057 (mmt) cc_final: 0.6775 (mmt) REVERT: L 61 MET cc_start: 0.6539 (mpp) cc_final: 0.5909 (mmm) REVERT: L 290 TYR cc_start: 0.8719 (m-80) cc_final: 0.8485 (m-80) REVERT: L 368 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6827 (mm-30) REVERT: L 548 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8079 (mtmt) REVERT: L 967 MET cc_start: 0.7634 (mtt) cc_final: 0.7290 (mtt) REVERT: L 973 MET cc_start: 0.8259 (mtt) cc_final: 0.7981 (mtt) REVERT: L 985 GLN cc_start: 0.8454 (tt0) cc_final: 0.8171 (tp40) REVERT: L 1380 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.6922 (mp) outliers start: 19 outliers final: 13 residues processed: 169 average time/residue: 0.1030 time to fit residues: 24.7457 Evaluate side-chains 168 residues out of total 1349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 349 ILE Chi-restraints excluded: chain L residue 548 LYS Chi-restraints excluded: chain L residue 878 SER Chi-restraints excluded: chain L residue 1004 VAL Chi-restraints excluded: chain L residue 1064 LEU Chi-restraints excluded: chain L residue 1069 THR Chi-restraints excluded: chain L residue 1115 MET Chi-restraints excluded: chain L residue 1119 THR Chi-restraints excluded: chain L residue 1359 THR Chi-restraints excluded: chain L residue 1380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1053 HIS ** L1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.199087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.159725 restraints weight = 26503.696| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 5.12 r_work: 0.3454 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12361 Z= 0.125 Angle : 0.554 8.465 16710 Z= 0.276 Chirality : 0.040 0.136 1907 Planarity : 0.004 0.064 2113 Dihedral : 3.995 27.139 1663 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.26 % Allowed : 19.41 % Favored : 79.33 % 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: 1.49 (0.22), residues: 1493 helix: 1.94 (0.18), residues: 851 sheet: -0.21 (0.52), residues: 101 loop : -0.26 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 465 TYR 0.017 0.002 TYR L 87 PHE 0.020 0.002 PHE L1191 TRP 0.038 0.001 TRP L1189 HIS 0.004 0.001 HIS L 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.12 (12354) covalent geometry : angle 0.55343 / 0.28 (16709) hydrogen bonds : bond 0.03077 / 2.00 ( 672) hydrogen bonds : angle 3.87141 / 2.80 ( 1936) metal coordination : bond 0.00174 / 0.08 ( 7) metal coordination : angle 2.47748 / 1.30 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.64 seconds wall clock time: 45 minutes 50.81 seconds (2750.81 seconds total)