Starting phenix.real_space_refine on Thu Jul 31 04:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.cif Found real_map, /net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.map" model { file = "/net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9knq_62459/07_2025/9knq_62459.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 67 5.16 5 C 8032 2.51 5 N 2182 2.21 5 O 2323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12606 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1284, 10307 Classifications: {'peptide': 1284} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1230} Chain breaks: 3 Chain: "B" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 398 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "D" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 461 Classifications: {'peptide': 61} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 56} Chain: "E" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 328 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "C" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1110 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain breaks: 2 Chain: "A" 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 8824 SG CYS A1177 19.444 78.700 131.175 1.00168.52 S ATOM 8458 SG CYS A1132 42.669 80.665 138.949 1.00139.91 S ATOM 10030 SG CYS A1369 38.573 81.979 139.175 1.00183.45 S ATOM 10036 SG CYS A1370 40.325 80.918 136.262 1.00177.75 S Time building chain proxies: 7.60, per 1000 atoms: 0.60 Number of scatterers: 12606 At special positions: 0 Unit cell: (98.3586, 109.93, 166.824, 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 67 16.00 O 2323 8.00 N 2182 7.00 C 8032 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" NE2 HIS A1364 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1177 " pdb=" ZN A2202 " pdb="ZN ZN A2202 " - pdb=" SG CYS A1370 " pdb="ZN ZN A2202 " - pdb=" SG CYS A1369 " pdb="ZN ZN A2202 " - pdb=" SG CYS A1132 " 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 58.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.105A pdb=" N ILE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 103 through 136 removed outlier: 3.686A pdb=" N ARG A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.639A pdb=" N TYR A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 3.819A pdb=" N HIS A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Processing helix chain 'A' and resid 251 through 267 removed outlier: 4.357A pdb=" N GLY A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.981A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.793A pdb=" N SER A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.630A pdb=" N THR A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 4.123A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.889A pdb=" N GLY A 347 " --> pdb=" O HIS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 363 through 375 removed outlier: 4.121A pdb=" N TYR A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.688A pdb=" N CYS A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.578A pdb=" N ALA A 444 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 472 through 479 removed outlier: 6.219A pdb=" N ASP A 477 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.742A pdb=" N MET A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 672 through 688 removed outlier: 5.210A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.912A pdb=" N LYS A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 removed outlier: 4.054A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.747A pdb=" N ASP A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 814 " --> pdb=" O ARG A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.994A pdb=" N SER A 849 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 880 Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 913 through 923 removed outlier: 3.647A pdb=" N ILE A 918 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Proline residue: A 919 - end of helix Processing helix chain 'A' and resid 923 through 933 removed outlier: 4.127A pdb=" N LEU A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 removed outlier: 3.795A pdb=" N ILE A 937 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 955 through 970 Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.620A pdb=" N ILE A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1051 Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1067 through 1079 removed outlier: 3.517A pdb=" N ALA A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1096 through 1120 removed outlier: 5.136A pdb=" N ASP A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1110 " --> pdb=" O TYR A1106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A1111 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1145 removed outlier: 3.675A pdb=" N HIS A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1233 through 1237 removed outlier: 4.628A pdb=" N ARG A1236 " --> pdb=" O ARG A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1250 removed outlier: 3.822A pdb=" N SER A1246 " --> pdb=" O ALA A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1265 Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1306 through 1311 removed outlier: 3.693A pdb=" N ARG A1309 " --> pdb=" O ARG A1306 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A1311 " --> pdb=" O ALA A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1348 removed outlier: 4.187A pdb=" N GLY A1336 " --> pdb=" O ILE A1332 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 368 removed outlier: 4.567A pdb=" N SER B 334 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 344 Processing helix chain 'D' and resid 345 through 373 removed outlier: 4.052A pdb=" N ALA D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 369 removed outlier: 4.354A pdb=" N LYS E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG E 355 " --> pdb=" O LYS E 351 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER E 369 " --> pdb=" O GLY E 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 4.487A pdb=" N LEU C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 370 removed outlier: 3.828A pdb=" N THR C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 4.380A pdb=" N ARG C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 488 removed outlier: 4.008A pdb=" N ASP C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.663A pdb=" N LYS C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.439A pdb=" N SER A 83 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N TYR A 222 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS A 219 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 203 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381 removed outlier: 3.526A pdb=" N LYS A 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 534 Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 771 removed outlier: 3.692A pdb=" N ARG A 765 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 829 through 832 removed outlier: 3.608A pdb=" N GLY A 835 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1166 through 1171 removed outlier: 4.153A pdb=" N THR A1359 " --> pdb=" O VAL A1192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1192 " --> pdb=" O THR A1359 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4106 1.34 - 1.46: 2203 1.46 - 1.58: 6430 1.58 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 12848 Sorted by residual: bond pdb=" N PRO A 409 " pdb=" CA PRO A 409 " ideal model delta sigma weight residual 1.465 1.487 -0.022 2.03e-02 2.43e+03 1.16e+00 bond pdb=" C ILE D 374 " pdb=" N PRO D 375 " ideal model delta sigma weight residual 1.338 1.356 -0.018 1.90e-02 2.77e+03 9.46e-01 bond pdb=" CA PRO D 375 " pdb=" CB PRO D 375 " ideal model delta sigma weight residual 1.533 1.516 0.017 1.80e-02 3.09e+03 8.84e-01 bond pdb=" C LYS C 489 " pdb=" N GLY C 490 " ideal model delta sigma weight residual 1.322 1.332 -0.010 1.20e-02 6.94e+03 6.68e-01 bond pdb=" CG PRO D 381 " pdb=" CD PRO D 381 " ideal model delta sigma weight residual 1.503 1.530 -0.027 3.40e-02 8.65e+02 6.46e-01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 17227 2.73 - 5.45: 131 5.45 - 8.18: 10 8.18 - 10.90: 1 10.90 - 13.63: 2 Bond angle restraints: 17371 Sorted by residual: angle pdb=" C ILE D 374 " pdb=" N PRO D 375 " pdb=" CA PRO D 375 " ideal model delta sigma weight residual 127.00 140.63 -13.63 2.40e+00 1.74e-01 3.22e+01 angle pdb=" C ILE D 374 " pdb=" N PRO D 375 " pdb=" CD PRO D 375 " ideal model delta sigma weight residual 120.60 109.34 11.26 2.20e+00 2.07e-01 2.62e+01 angle pdb=" C ILE A 879 " pdb=" N GLU A 880 " pdb=" CA GLU A 880 " ideal model delta sigma weight residual 122.31 114.93 7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C ASP A 728 " pdb=" N GLN A 729 " pdb=" CA GLN A 729 " ideal model delta sigma weight residual 121.54 128.15 -6.61 1.91e+00 2.74e-01 1.20e+01 angle pdb=" N ILE A 752 " pdb=" CA ILE A 752 " pdb=" C ILE A 752 " ideal model delta sigma weight residual 108.88 115.12 -6.24 2.16e+00 2.14e-01 8.35e+00 ... (remaining 17366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6815 17.78 - 35.57: 778 35.57 - 53.35: 184 53.35 - 71.14: 42 71.14 - 88.92: 12 Dihedral angle restraints: 7831 sinusoidal: 3208 harmonic: 4623 Sorted by residual: dihedral pdb=" CA ASN A1330 " pdb=" C ASN A1330 " pdb=" N PHE A1331 " pdb=" CA PHE A1331 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASN A 727 " pdb=" C ASN A 727 " pdb=" N ASP A 728 " pdb=" CA ASP A 728 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP D 387 " pdb=" C ASP D 387 " pdb=" N VAL D 388 " pdb=" CA VAL D 388 " ideal model delta harmonic sigma weight residual 180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 7828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1183 0.031 - 0.061: 534 0.061 - 0.092: 189 0.092 - 0.123: 70 0.123 - 0.153: 16 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CB ILE A1171 " pdb=" CA ILE A1171 " pdb=" CG1 ILE A1171 " pdb=" CG2 ILE A1171 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE A 732 " pdb=" N ILE A 732 " pdb=" C ILE A 732 " pdb=" CB ILE A 732 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CB ILE B 358 " pdb=" CA ILE B 358 " pdb=" CG1 ILE B 358 " pdb=" CG2 ILE B 358 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1989 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 274 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.72e+00 pdb=" N PRO A 275 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 408 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 409 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 787 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 788 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 788 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 788 " -0.018 5.00e-02 4.00e+02 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 158 2.62 - 3.19: 11273 3.19 - 3.76: 18178 3.76 - 4.33: 23790 4.33 - 4.90: 40169 Nonbonded interactions: 93568 Sorted by model distance: nonbonded pdb=" OD1 ASN A 132 " pdb=" OH TYR A 886 " model vdw 2.049 3.040 nonbonded pdb=" O LEU A1318 " pdb=" OH TYR A1333 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLN A1007 " pdb=" OH TYR A1106 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OD1 ASP A 335 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP A 99 " pdb=" OG SER A 102 " model vdw 2.261 3.040 ... (remaining 93563 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 333 through 380) selection = (chain 'D' and resid 333 through 380) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.007 0.622 12853 Z= 0.264 Angle : 0.645 13.625 17371 Z= 0.360 Chirality : 0.042 0.153 1992 Planarity : 0.003 0.041 2195 Dihedral : 16.140 88.922 4837 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.94 % Allowed : 23.64 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1561 helix: -0.24 (0.17), residues: 834 sheet: -1.14 (0.57), residues: 85 loop : -3.74 (0.20), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1189 HIS 0.005 0.001 HIS A1053 PHE 0.013 0.001 PHE A 546 TYR 0.015 0.001 TYR A1108 ARG 0.002 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.09138 ( 641) hydrogen bonds : angle 4.09847 ( 1857) metal coordination : bond 0.30368 ( 5) covalent geometry : bond 0.00389 (12848) covalent geometry : angle 0.64518 (17371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 194 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8381 (mm) REVERT: A 1184 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7721 (t) REVERT: A 1272 GLU cc_start: 0.9048 (mp0) cc_final: 0.8847 (mp0) REVERT: A 1345 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8728 (tp30) REVERT: A 1351 GLU cc_start: 0.8381 (pt0) cc_final: 0.7941 (pm20) REVERT: A 1374 MET cc_start: 0.7384 (pp-130) cc_final: 0.7094 (pp-130) REVERT: E 350 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8142 (mmtp) REVERT: E 355 ARG cc_start: 0.8860 (ptp90) cc_final: 0.8470 (ttp80) REVERT: C 338 SER cc_start: 0.4564 (OUTLIER) cc_final: 0.4347 (p) REVERT: C 477 ARG cc_start: 0.9127 (mtp180) cc_final: 0.8857 (mtp180) outliers start: 98 outliers final: 39 residues processed: 274 average time/residue: 1.1994 time to fit residues: 358.9258 Evaluate side-chains 207 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 SER Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1330 ASN Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain E residue 350 LYS Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 397 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 187 HIS A 404 HIS A 425 GLN A 729 GLN A 744 GLN A 771 GLN A 845 GLN A1362 HIS E 352 GLN E 354 ASN ** E 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.064278 restraints weight = 25633.007| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.81 r_work: 0.2654 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12853 Z= 0.180 Angle : 0.631 10.190 17371 Z= 0.324 Chirality : 0.042 0.204 1992 Planarity : 0.004 0.039 2195 Dihedral : 7.308 59.765 1795 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.30 % Allowed : 25.76 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1561 helix: 0.84 (0.19), residues: 833 sheet: -0.64 (0.58), residues: 84 loop : -3.20 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1247 HIS 0.009 0.001 HIS A1066 PHE 0.014 0.001 PHE A 451 TYR 0.016 0.001 TYR A 837 ARG 0.007 0.000 ARG A1019 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 641) hydrogen bonds : angle 3.93896 ( 1857) metal coordination : bond 0.00229 ( 5) covalent geometry : bond 0.00429 (12848) covalent geometry : angle 0.63148 (17371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 174 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ILE cc_start: 0.9250 (pt) cc_final: 0.8871 (pp) REVERT: A 465 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8361 (mmtt) REVERT: A 539 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 1007 GLN cc_start: 0.8592 (mp10) cc_final: 0.8187 (mp10) REVERT: A 1121 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8431 (ttp80) REVERT: A 1374 MET cc_start: 0.6930 (pp-130) cc_final: 0.6685 (pp-130) REVERT: B 352 GLN cc_start: 0.7290 (tm130) cc_final: 0.6882 (tm130) REVERT: B 355 ARG cc_start: 0.8705 (ppt90) cc_final: 0.8453 (ppt170) REVERT: D 354 ASN cc_start: 0.8874 (m-40) cc_final: 0.8273 (t0) REVERT: D 355 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8658 (mmm-85) REVERT: E 355 ARG cc_start: 0.8878 (ptp90) cc_final: 0.8501 (ttp80) REVERT: C 408 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6599 (mm-30) outliers start: 89 outliers final: 39 residues processed: 242 average time/residue: 1.4355 time to fit residues: 381.6772 Evaluate side-chains 199 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 402 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 134 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 GLN A1110 GLN A1317 ASN A1377 HIS C 498 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.064630 restraints weight = 25746.837| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.72 r_work: 0.2658 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12853 Z= 0.177 Angle : 0.621 8.710 17371 Z= 0.319 Chirality : 0.043 0.258 1992 Planarity : 0.004 0.038 2195 Dihedral : 6.135 59.278 1753 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 7.64 % Allowed : 24.70 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1561 helix: 1.21 (0.19), residues: 830 sheet: -0.39 (0.59), residues: 86 loop : -2.93 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.006 0.001 HIS A1066 PHE 0.012 0.001 PHE A 451 TYR 0.014 0.001 TYR A 832 ARG 0.005 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 641) hydrogen bonds : angle 3.90174 ( 1857) metal coordination : bond 0.00310 ( 5) covalent geometry : bond 0.00422 (12848) covalent geometry : angle 0.62060 (17371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 160 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ILE cc_start: 0.9211 (pt) cc_final: 0.8826 (pp) REVERT: A 461 THR cc_start: 0.9165 (p) cc_final: 0.8303 (m) REVERT: A 465 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8098 (mmtt) REVERT: A 539 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8242 (mm) REVERT: A 771 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: A 945 MET cc_start: 0.8915 (mtt) cc_final: 0.8575 (mtm) REVERT: A 1007 GLN cc_start: 0.8588 (mp10) cc_final: 0.8242 (mp10) REVERT: A 1078 MET cc_start: 0.8122 (ttm) cc_final: 0.7804 (ttt) REVERT: A 1121 ARG cc_start: 0.8735 (ttp80) cc_final: 0.8521 (ttp80) REVERT: A 1181 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: A 1374 MET cc_start: 0.6929 (pp-130) cc_final: 0.6658 (pp-130) REVERT: A 1392 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8683 (pp) REVERT: B 379 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: D 354 ASN cc_start: 0.8958 (m-40) cc_final: 0.8449 (t0) REVERT: D 355 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (mmm-85) REVERT: E 355 ARG cc_start: 0.8892 (ptp90) cc_final: 0.8491 (ttp80) REVERT: C 408 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6562 (mm-30) REVERT: C 475 GLU cc_start: 0.9056 (tp30) cc_final: 0.8504 (tm-30) outliers start: 108 outliers final: 53 residues processed: 241 average time/residue: 1.0220 time to fit residues: 272.9664 Evaluate side-chains 213 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1314 SER Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 GLN D 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.064203 restraints weight = 25650.622| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.69 r_work: 0.2648 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12853 Z= 0.196 Angle : 0.632 7.582 17371 Z= 0.324 Chirality : 0.043 0.255 1992 Planarity : 0.004 0.039 2195 Dihedral : 6.119 58.949 1752 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 7.57 % Allowed : 24.98 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1561 helix: 1.20 (0.19), residues: 840 sheet: -0.27 (0.59), residues: 86 loop : -2.90 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.009 0.001 HIS C 498 PHE 0.014 0.001 PHE A 546 TYR 0.015 0.001 TYR A 837 ARG 0.005 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 641) hydrogen bonds : angle 3.94329 ( 1857) metal coordination : bond 0.00366 ( 5) covalent geometry : bond 0.00472 (12848) covalent geometry : angle 0.63204 (17371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 161 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 284 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 380 ILE cc_start: 0.9184 (pt) cc_final: 0.8792 (pp) REVERT: A 461 THR cc_start: 0.9145 (p) cc_final: 0.8240 (m) REVERT: A 465 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8067 (mmtt) REVERT: A 539 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8234 (mm) REVERT: A 561 GLU cc_start: 0.8355 (tt0) cc_final: 0.8046 (tp30) REVERT: A 771 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: A 839 ASP cc_start: 0.9139 (t0) cc_final: 0.8800 (t0) REVERT: A 1007 GLN cc_start: 0.8630 (mp10) cc_final: 0.8256 (mp10) REVERT: A 1078 MET cc_start: 0.8014 (ttm) cc_final: 0.7769 (ttt) REVERT: A 1181 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: A 1374 MET cc_start: 0.6883 (pp-130) cc_final: 0.6591 (pp-130) REVERT: A 1392 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8790 (pp) REVERT: B 379 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8522 (ttpp) REVERT: D 354 ASN cc_start: 0.8943 (m-40) cc_final: 0.8436 (t0) REVERT: D 355 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8667 (mmm-85) REVERT: E 337 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: E 355 ARG cc_start: 0.8877 (ptp90) cc_final: 0.8463 (ttp80) REVERT: C 408 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6655 (tp30) REVERT: C 411 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6338 (mtmt) REVERT: C 475 GLU cc_start: 0.9070 (tp30) cc_final: 0.8538 (tm-30) REVERT: C 499 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8860 (mt0) outliers start: 107 outliers final: 63 residues processed: 243 average time/residue: 1.0802 time to fit residues: 290.2193 Evaluate side-chains 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 499 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 8 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 352 GLN E 356 GLN ** C 356 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.100552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.066384 restraints weight = 25308.859| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.73 r_work: 0.2678 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12853 Z= 0.145 Angle : 0.591 8.523 17371 Z= 0.304 Chirality : 0.042 0.305 1992 Planarity : 0.004 0.038 2195 Dihedral : 5.854 58.717 1750 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.86 % Allowed : 26.26 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1561 helix: 1.34 (0.19), residues: 844 sheet: -0.27 (0.59), residues: 86 loop : -2.75 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.007 0.001 HIS C 498 PHE 0.011 0.001 PHE A 451 TYR 0.013 0.001 TYR A 832 ARG 0.006 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.04915 ( 641) hydrogen bonds : angle 3.79835 ( 1857) metal coordination : bond 0.00347 ( 5) covalent geometry : bond 0.00339 (12848) covalent geometry : angle 0.59145 (17371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 165 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 284 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8811 (tm-30) REVERT: A 380 ILE cc_start: 0.9173 (pt) cc_final: 0.8796 (pp) REVERT: A 461 THR cc_start: 0.9130 (p) cc_final: 0.8164 (m) REVERT: A 465 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8089 (mmtt) REVERT: A 539 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 561 GLU cc_start: 0.8325 (tt0) cc_final: 0.8018 (tp30) REVERT: A 771 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: A 773 ASP cc_start: 0.8941 (p0) cc_final: 0.8570 (p0) REVERT: A 839 ASP cc_start: 0.9136 (t0) cc_final: 0.8775 (t0) REVERT: A 1007 GLN cc_start: 0.8608 (mp10) cc_final: 0.8080 (mp10) REVERT: A 1181 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: A 1331 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.7035 (p90) REVERT: A 1374 MET cc_start: 0.6898 (pp-130) cc_final: 0.6618 (pp-130) REVERT: B 356 GLN cc_start: 0.7405 (tt0) cc_final: 0.6990 (tp40) REVERT: B 379 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8464 (ttpp) REVERT: D 354 ASN cc_start: 0.8944 (m-40) cc_final: 0.8582 (t0) REVERT: D 355 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.8665 (mmm-85) REVERT: E 337 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: E 355 ARG cc_start: 0.8932 (ptp90) cc_final: 0.8531 (ttp80) REVERT: C 356 GLN cc_start: 0.7819 (mt0) cc_final: 0.7324 (tt0) REVERT: C 408 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6712 (tp30) REVERT: C 411 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.6124 (mtmt) REVERT: C 475 GLU cc_start: 0.9066 (tp30) cc_final: 0.8508 (tm-30) REVERT: C 499 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8807 (mt0) outliers start: 97 outliers final: 54 residues processed: 234 average time/residue: 1.1647 time to fit residues: 302.8008 Evaluate side-chains 216 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 771 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1240 ARG Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 HIS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 499 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 771 GLN A1053 HIS D 352 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067393 restraints weight = 25278.732| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.73 r_work: 0.2696 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12853 Z= 0.130 Angle : 0.594 9.062 17371 Z= 0.300 Chirality : 0.041 0.297 1992 Planarity : 0.004 0.038 2195 Dihedral : 5.711 58.323 1750 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.16 % Allowed : 27.11 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1561 helix: 1.44 (0.19), residues: 844 sheet: -0.16 (0.59), residues: 86 loop : -2.65 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.008 0.001 HIS C 498 PHE 0.011 0.001 PHE A 451 TYR 0.017 0.001 TYR A 837 ARG 0.006 0.000 ARG C 479 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 641) hydrogen bonds : angle 3.71130 ( 1857) metal coordination : bond 0.00333 ( 5) covalent geometry : bond 0.00301 (12848) covalent geometry : angle 0.59381 (17371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 163 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 284 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 380 ILE cc_start: 0.9192 (pt) cc_final: 0.8841 (pp) REVERT: A 461 THR cc_start: 0.9213 (p) cc_final: 0.8787 (m) REVERT: A 539 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 561 GLU cc_start: 0.8324 (tt0) cc_final: 0.8029 (tp30) REVERT: A 839 ASP cc_start: 0.9116 (t0) cc_final: 0.8742 (t0) REVERT: A 854 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8921 (m) REVERT: A 1007 GLN cc_start: 0.8611 (mp10) cc_final: 0.8195 (mp10) REVERT: A 1173 ARG cc_start: 0.8965 (pmm-80) cc_final: 0.8499 (pmm-80) REVERT: A 1181 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: A 1331 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.7068 (p90) REVERT: A 1374 MET cc_start: 0.6902 (pp-130) cc_final: 0.6602 (pp-130) REVERT: B 356 GLN cc_start: 0.7363 (tt0) cc_final: 0.6804 (tt0) REVERT: D 354 ASN cc_start: 0.8950 (m-40) cc_final: 0.8528 (t0) REVERT: D 355 ARG cc_start: 0.8934 (mmm-85) cc_final: 0.8669 (mmm-85) REVERT: D 387 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6586 (p0) REVERT: E 337 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: E 355 ARG cc_start: 0.8956 (ptp90) cc_final: 0.8559 (ttp80) REVERT: E 356 GLN cc_start: 0.8384 (mt0) cc_final: 0.8101 (mm-40) REVERT: C 356 GLN cc_start: 0.7806 (mt0) cc_final: 0.7330 (tt0) REVERT: C 411 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.6171 (mtmt) REVERT: C 475 GLU cc_start: 0.9087 (tp30) cc_final: 0.8534 (tm-30) REVERT: C 499 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8814 (mt0) outliers start: 87 outliers final: 50 residues processed: 230 average time/residue: 1.2469 time to fit residues: 316.5703 Evaluate side-chains 208 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 387 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 499 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 0.0770 chunk 126 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN A 771 GLN D 352 GLN E 366 HIS C 352 GLN ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.067013 restraints weight = 25273.109| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.77 r_work: 0.2706 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12853 Z= 0.126 Angle : 0.600 9.002 17371 Z= 0.303 Chirality : 0.041 0.308 1992 Planarity : 0.004 0.038 2195 Dihedral : 5.349 58.013 1744 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.87 % Allowed : 28.31 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1561 helix: 1.53 (0.19), residues: 843 sheet: 0.01 (0.59), residues: 86 loop : -2.52 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1189 HIS 0.009 0.001 HIS C 498 PHE 0.010 0.001 PHE A 451 TYR 0.015 0.001 TYR A1245 ARG 0.008 0.000 ARG A1240 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 641) hydrogen bonds : angle 3.66680 ( 1857) metal coordination : bond 0.00374 ( 5) covalent geometry : bond 0.00293 (12848) covalent geometry : angle 0.60020 (17371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 160 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 284 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8839 (tm-30) REVERT: A 311 GLU cc_start: 0.9384 (tp30) cc_final: 0.9140 (tp30) REVERT: A 380 ILE cc_start: 0.9215 (pt) cc_final: 0.8871 (pp) REVERT: A 539 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8147 (mm) REVERT: A 561 GLU cc_start: 0.8398 (tt0) cc_final: 0.8144 (tp30) REVERT: A 839 ASP cc_start: 0.9094 (t0) cc_final: 0.8721 (t0) REVERT: A 913 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 1007 GLN cc_start: 0.8608 (mp10) cc_final: 0.8186 (mp10) REVERT: A 1078 MET cc_start: 0.8786 (tmm) cc_final: 0.8539 (tmm) REVERT: A 1173 ARG cc_start: 0.8953 (pmm-80) cc_final: 0.8497 (pmm-80) REVERT: A 1181 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: A 1331 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7040 (p90) REVERT: A 1374 MET cc_start: 0.6785 (pp-130) cc_final: 0.6467 (pp-130) REVERT: D 354 ASN cc_start: 0.8966 (m-40) cc_final: 0.8558 (t0) REVERT: D 355 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8678 (mmm-85) REVERT: E 337 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: E 355 ARG cc_start: 0.8955 (ptp90) cc_final: 0.8573 (ttp80) REVERT: C 357 ASN cc_start: 0.8040 (m-40) cc_final: 0.7815 (m110) REVERT: C 411 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6190 (mtmt) REVERT: C 475 GLU cc_start: 0.9137 (tp30) cc_final: 0.8623 (tm-30) REVERT: C 499 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8804 (mt0) outliers start: 83 outliers final: 51 residues processed: 224 average time/residue: 1.0841 time to fit residues: 268.3692 Evaluate side-chains 212 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 153 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 499 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 137 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN E 357 ASN C 352 GLN ** C 356 GLN ** 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 = 0.3452 r_free = 0.3452 target = 0.100322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.066698 restraints weight = 25077.012| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.66 r_work: 0.2685 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12853 Z= 0.168 Angle : 0.635 11.408 17371 Z= 0.318 Chirality : 0.043 0.332 1992 Planarity : 0.004 0.039 2195 Dihedral : 5.363 58.769 1741 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.45 % Allowed : 28.80 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1561 helix: 1.42 (0.19), residues: 845 sheet: 0.06 (0.60), residues: 86 loop : -2.49 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.008 0.001 HIS C 498 PHE 0.011 0.001 PHE A 451 TYR 0.023 0.002 TYR A 463 ARG 0.007 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 641) hydrogen bonds : angle 3.78455 ( 1857) metal coordination : bond 0.00388 ( 5) covalent geometry : bond 0.00402 (12848) covalent geometry : angle 0.63500 (17371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 151 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9340 (t70) cc_final: 0.9036 (t0) REVERT: A 174 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 284 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8802 (tm-30) REVERT: A 311 GLU cc_start: 0.9388 (tp30) cc_final: 0.9150 (tp30) REVERT: A 380 ILE cc_start: 0.9217 (pt) cc_final: 0.8859 (pp) REVERT: A 465 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8584 (mmpt) REVERT: A 539 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 561 GLU cc_start: 0.8356 (tt0) cc_final: 0.8062 (tp30) REVERT: A 839 ASP cc_start: 0.9106 (t0) cc_final: 0.8759 (t0) REVERT: A 913 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 1007 GLN cc_start: 0.8654 (mp10) cc_final: 0.8242 (mp10) REVERT: A 1173 ARG cc_start: 0.8949 (pmm-80) cc_final: 0.8491 (pmm-80) REVERT: A 1181 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: A 1331 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6929 (p90) REVERT: A 1374 MET cc_start: 0.6815 (pp-130) cc_final: 0.6537 (pp-130) REVERT: D 354 ASN cc_start: 0.8967 (m-40) cc_final: 0.8542 (t0) REVERT: D 355 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8684 (mmm-85) REVERT: E 337 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: E 355 ARG cc_start: 0.9006 (ptp90) cc_final: 0.8600 (ttp80) REVERT: C 357 ASN cc_start: 0.8097 (m-40) cc_final: 0.7852 (m110) REVERT: C 411 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6339 (mtmt) REVERT: C 475 GLU cc_start: 0.9159 (tp30) cc_final: 0.8658 (tm-30) outliers start: 77 outliers final: 47 residues processed: 209 average time/residue: 1.6500 time to fit residues: 382.0541 Evaluate side-chains 203 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 455 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** E 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** 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 = 0.3435 r_free = 0.3435 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.065671 restraints weight = 25354.880| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.62 r_work: 0.2660 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12853 Z= 0.193 Angle : 0.669 11.990 17371 Z= 0.336 Chirality : 0.044 0.310 1992 Planarity : 0.004 0.039 2195 Dihedral : 5.467 58.661 1740 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.02 % Allowed : 29.37 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1561 helix: 1.35 (0.19), residues: 850 sheet: 0.06 (0.60), residues: 86 loop : -2.53 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1189 HIS 0.008 0.001 HIS C 498 PHE 0.012 0.001 PHE A 451 TYR 0.021 0.002 TYR A 463 ARG 0.007 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.05446 ( 641) hydrogen bonds : angle 3.90219 ( 1857) metal coordination : bond 0.00451 ( 5) covalent geometry : bond 0.00464 (12848) covalent geometry : angle 0.66870 (17371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 156 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9340 (t70) cc_final: 0.9002 (t0) REVERT: A 174 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 284 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8811 (tm-30) REVERT: A 311 GLU cc_start: 0.9401 (tp30) cc_final: 0.9140 (tp30) REVERT: A 380 ILE cc_start: 0.9184 (pt) cc_final: 0.8795 (pp) REVERT: A 465 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8647 (mmmm) REVERT: A 539 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8215 (mm) REVERT: A 561 GLU cc_start: 0.8370 (tt0) cc_final: 0.8062 (tp30) REVERT: A 839 ASP cc_start: 0.9163 (t0) cc_final: 0.8792 (t0) REVERT: A 913 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 1007 GLN cc_start: 0.8658 (mp10) cc_final: 0.8209 (mp10) REVERT: A 1173 ARG cc_start: 0.8952 (pmm-80) cc_final: 0.8515 (pmm-80) REVERT: A 1181 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: A 1331 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6968 (p90) REVERT: A 1374 MET cc_start: 0.6801 (pp-130) cc_final: 0.6530 (pp-130) REVERT: D 354 ASN cc_start: 0.8967 (m-40) cc_final: 0.8531 (t0) REVERT: D 355 ARG cc_start: 0.8957 (mmm-85) cc_final: 0.8707 (mmm-85) REVERT: E 337 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: E 355 ARG cc_start: 0.8981 (ptp90) cc_final: 0.8570 (ttp80) REVERT: C 357 ASN cc_start: 0.8119 (m-40) cc_final: 0.7861 (m110) REVERT: C 411 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6354 (mtmt) REVERT: C 475 GLU cc_start: 0.9135 (tp30) cc_final: 0.8645 (tm-30) outliers start: 71 outliers final: 50 residues processed: 212 average time/residue: 1.1891 time to fit residues: 277.9391 Evaluate side-chains 204 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1000 SER Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 455 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** C 356 GLN ** 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 = 0.3490 r_free = 0.3490 target = 0.102924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.069038 restraints weight = 24763.491| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.68 r_work: 0.2734 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12853 Z= 0.117 Angle : 0.643 11.881 17371 Z= 0.315 Chirality : 0.042 0.337 1992 Planarity : 0.004 0.058 2195 Dihedral : 5.250 56.994 1740 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.40 % Allowed : 30.93 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1561 helix: 1.54 (0.19), residues: 849 sheet: 0.12 (0.59), residues: 86 loop : -2.41 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1260 HIS 0.007 0.001 HIS C 498 PHE 0.009 0.001 PHE A 451 TYR 0.021 0.001 TYR A 463 ARG 0.007 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 641) hydrogen bonds : angle 3.67783 ( 1857) metal coordination : bond 0.00402 ( 5) covalent geometry : bond 0.00262 (12848) covalent geometry : angle 0.64341 (17371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.9355 (t70) cc_final: 0.9005 (t0) REVERT: A 174 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8329 (tm-30) REVERT: A 284 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 380 ILE cc_start: 0.9195 (pt) cc_final: 0.8856 (pp) REVERT: A 539 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 561 GLU cc_start: 0.8369 (tt0) cc_final: 0.8129 (tp30) REVERT: A 839 ASP cc_start: 0.9116 (t0) cc_final: 0.8754 (t0) REVERT: A 913 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8651 (p) REVERT: A 1007 GLN cc_start: 0.8599 (mp10) cc_final: 0.8168 (mp10) REVERT: A 1173 ARG cc_start: 0.8889 (pmm-80) cc_final: 0.8530 (pmm-80) REVERT: A 1331 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6826 (p90) REVERT: A 1374 MET cc_start: 0.6829 (pp-130) cc_final: 0.6562 (pp-130) REVERT: B 377 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8344 (mt) REVERT: D 354 ASN cc_start: 0.8945 (m-40) cc_final: 0.8501 (t0) REVERT: D 355 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8665 (mmm-85) REVERT: E 337 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: E 355 ARG cc_start: 0.8947 (ptp90) cc_final: 0.8537 (ttp80) REVERT: C 357 ASN cc_start: 0.8091 (m-40) cc_final: 0.7823 (m110) REVERT: C 475 GLU cc_start: 0.9151 (tp30) cc_final: 0.8646 (tm-30) outliers start: 48 outliers final: 38 residues processed: 198 average time/residue: 1.1603 time to fit residues: 252.0579 Evaluate side-chains 194 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 892 ASN Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1241 ILE Chi-restraints excluded: chain A residue 1246 SER Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 488 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 131 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.069009 restraints weight = 24932.935| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.73 r_work: 0.2732 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12853 Z= 0.124 Angle : 0.665 14.749 17371 Z= 0.324 Chirality : 0.043 0.331 1992 Planarity : 0.004 0.038 2195 Dihedral : 5.214 56.320 1739 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.68 % Allowed : 31.14 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1561 helix: 1.56 (0.19), residues: 848 sheet: 0.22 (0.59), residues: 86 loop : -2.33 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1189 HIS 0.007 0.001 HIS C 498 PHE 0.009 0.001 PHE A 451 TYR 0.022 0.001 TYR A 463 ARG 0.007 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 641) hydrogen bonds : angle 3.69434 ( 1857) metal coordination : bond 0.00399 ( 5) covalent geometry : bond 0.00283 (12848) covalent geometry : angle 0.66494 (17371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10002.02 seconds wall clock time: 180 minutes 41.73 seconds (10841.73 seconds total)