Starting phenix.real_space_refine on Sat May 2 18:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.map" model { file = "/net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vre_65285/05_2026/9vre_65285.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 P 6 5.49 5 S 47 5.16 5 C 5084 2.51 5 N 1321 2.21 5 O 1440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7898 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7862 Classifications: {'peptide': 997} Link IDs: {'PTRANS': 40, 'TRANS': 956} Chain breaks: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.22 Number of scatterers: 7898 At special positions: 0 Unit cell: (75.808, 101.352, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 6 15.00 O 1440 8.00 N 1321 7.00 C 5084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 220.2 milliseconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 76.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.695A pdb=" N GLN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.642A pdb=" N ILE A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 289 removed outlier: 3.550A pdb=" N ARG A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.599A pdb=" N LYS A 302 " --> pdb=" O TRP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.620A pdb=" N GLY A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 392 removed outlier: 3.706A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.668A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.715A pdb=" N MET A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.555A pdb=" N TYR A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 422 No H-bonds generated for 'chain 'A' and resid 421 through 422' Processing helix chain 'A' and resid 423 through 424 No H-bonds generated for 'chain 'A' and resid 423 through 424' Processing helix chain 'A' and resid 425 through 445 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 448 through 494 removed outlier: 3.630A pdb=" N VAL A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.741A pdb=" N GLU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 476 " --> pdb=" O HIS A 472 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 503 through 554 removed outlier: 3.914A pdb=" N LYS A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP A 521 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Proline residue: A 540 - end of helix Processing helix chain 'A' and resid 559 through 578 removed outlier: 4.384A pdb=" N ARG A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Proline residue: A 576 - end of helix Processing helix chain 'A' and resid 579 through 602 Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'A' and resid 755 through 765 removed outlier: 3.593A pdb=" N GLN A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 935 removed outlier: 3.831A pdb=" N TYR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 941 through 967 removed outlier: 3.707A pdb=" N LEU A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1025 Processing helix chain 'A' and resid 1028 through 1035 Processing helix chain 'A' and resid 1036 through 1054 removed outlier: 3.865A pdb=" N ILE A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1080 removed outlier: 3.905A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1080 " --> pdb=" O MET A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1116 removed outlier: 4.179A pdb=" N ILE A1085 " --> pdb=" O TRP A1081 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Proline residue: A1089 - end of helix removed outlier: 3.616A pdb=" N ALA A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER A1104 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A1110 " --> pdb=" O ARG A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1129 removed outlier: 4.759A pdb=" N ILE A1120 " --> pdb=" O LYS A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1137 Processing helix chain 'A' and resid 1138 through 1188 Proline residue: A1156 - end of helix Processing helix chain 'A' and resid 1195 through 1207 Processing helix chain 'A' and resid 1208 through 1227 Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1303 through 1311 removed outlier: 4.308A pdb=" N GLN A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1337 Processing helix chain 'A' and resid 1353 through 1358 Processing helix chain 'A' and resid 1364 through 1375 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1386 through 1389 Processing helix chain 'A' and resid 1393 through 1397 Processing helix chain 'A' and resid 1400 through 1416 removed outlier: 3.706A pdb=" N LYS A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A1416 " --> pdb=" O ALA A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1456 through 1462 removed outlier: 3.523A pdb=" N ASP A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1486 removed outlier: 3.631A pdb=" N LEU A1483 " --> pdb=" O THR A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1497 removed outlier: 3.571A pdb=" N GLN A1493 " --> pdb=" O SER A1489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AA2, first strand: chain 'A' and resid 1285 through 1286 removed outlier: 4.486A pdb=" N LEU A1267 " --> pdb=" O GLY A1317 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY A1317 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1340 through 1342 removed outlier: 6.978A pdb=" N SER A1340 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASP A1423 " --> pdb=" O SER A1340 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A1342 " --> pdb=" O ASP A1423 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A1420 " --> pdb=" O CYS A1451 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE A1453 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A1422 " --> pdb=" O ILE A1453 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A1292 " --> pdb=" O THR A1452 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A1478 " --> pdb=" O VAL A1466 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A1476 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A1470 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1351 through 1352 533 hydrogen bonds defined for protein. 1566 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: 1.40 Time building geometry restraints manager: 0.77 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: 2505 1.34 - 1.46: 1696 1.46 - 1.58: 3776 1.58 - 1.70: 6 1.70 - 1.81: 78 Bond restraints: 8061 Sorted by residual: bond pdb=" O12 IHP A1601 " pdb=" P2 IHP A1601 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O15 IHP A1601 " pdb=" P5 IHP A1601 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O16 IHP A1601 " pdb=" P6 IHP A1601 " ideal model delta sigma weight residual 1.672 1.606 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O14 IHP A1601 " pdb=" P4 IHP A1601 " ideal model delta sigma weight residual 1.671 1.607 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O13 IHP A1601 " pdb=" P3 IHP A1601 " ideal model delta sigma weight residual 1.669 1.612 0.057 2.00e-02 2.50e+03 8.18e+00 ... (remaining 8056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10722 2.09 - 4.19: 195 4.19 - 6.28: 27 6.28 - 8.38: 2 8.38 - 10.47: 1 Bond angle restraints: 10947 Sorted by residual: angle pdb=" C1 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" C3 IHP A1601 " ideal model delta sigma weight residual 108.51 118.98 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C VAL A1114 " pdb=" CA VAL A1114 " pdb=" CB VAL A1114 " ideal model delta sigma weight residual 110.93 107.83 3.10 1.10e+00 8.26e-01 7.95e+00 angle pdb=" CA LYS A1446 " pdb=" CB LYS A1446 " pdb=" CG LYS A1446 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.51e+00 angle pdb=" C VAL A1265 " pdb=" CA VAL A1265 " pdb=" CB VAL A1265 " ideal model delta sigma weight residual 111.23 108.47 2.76 1.01e+00 9.80e-01 7.49e+00 angle pdb=" N TRP A1256 " pdb=" CA TRP A1256 " pdb=" C TRP A1256 " ideal model delta sigma weight residual 109.81 115.54 -5.73 2.21e+00 2.05e-01 6.73e+00 ... (remaining 10942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 4684 34.96 - 69.91: 170 69.91 - 104.87: 13 104.87 - 139.82: 4 139.82 - 174.78: 2 Dihedral angle restraints: 4873 sinusoidal: 1963 harmonic: 2910 Sorted by residual: dihedral pdb=" C4 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" C3 IHP A1601 " pdb=" O12 IHP A1601 " ideal model delta sinusoidal sigma weight residual 60.90 -124.32 -174.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C6 IHP A1601 " pdb=" C1 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" O12 IHP A1601 " ideal model delta sinusoidal sigma weight residual 61.05 -135.06 -163.89 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C1 IHP A1601 " pdb=" C5 IHP A1601 " pdb=" C6 IHP A1601 " pdb=" O15 IHP A1601 " ideal model delta sinusoidal sigma weight residual -175.62 -49.24 -126.38 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 4870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.992: 1269 0.992 - 1.983: 0 1.983 - 2.975: 0 2.975 - 3.967: 0 3.967 - 4.959: 4 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2 IHP A1601 " pdb=" C1 IHP A1601 " pdb=" C3 IHP A1601 " pdb=" O12 IHP A1601 " both_signs ideal model delta sigma weight residual False -2.52 2.44 -4.96 2.00e-01 2.50e+01 6.15e+02 chirality pdb=" C5 IHP A1601 " pdb=" C4 IHP A1601 " pdb=" C6 IHP A1601 " pdb=" O15 IHP A1601 " both_signs ideal model delta sigma weight residual False -2.42 2.50 -4.92 2.00e-01 2.50e+01 6.05e+02 chirality pdb=" C1 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" C6 IHP A1601 " pdb=" O11 IHP A1601 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.76 2.00e-01 2.50e+01 5.67e+02 ... (remaining 1270 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1256 " -0.016 2.00e-02 2.50e+03 1.72e-02 7.37e+00 pdb=" CG TRP A1256 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A1256 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A1256 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1256 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1256 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1256 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1256 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1256 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1256 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1442 " 0.197 9.50e-02 1.11e+02 8.85e-02 5.45e+00 pdb=" NE ARG A1442 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A1442 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A1442 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A1442 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 372 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" CG ASP A 372 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP A 372 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 372 " -0.009 2.00e-02 2.50e+03 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3429 2.93 - 3.42: 8706 3.42 - 3.91: 12774 3.91 - 4.41: 14489 4.41 - 4.90: 23809 Nonbonded interactions: 63207 Sorted by model distance: nonbonded pdb=" O12 IHP A1601 " pdb=" O13 IHP A1601 " model vdw 2.435 2.432 nonbonded pdb=" O TYR A 368 " pdb=" OD2 ASP A 372 " model vdw 2.454 3.040 nonbonded pdb=" O11 IHP A1601 " pdb=" O12 IHP A1601 " model vdw 2.471 2.432 nonbonded pdb=" O ASP A1389 " pdb=" OD1 ASP A1389 " model vdw 2.476 3.040 nonbonded pdb=" O GLN A 754 " pdb=" OE1 GLN A 754 " model vdw 2.483 3.040 ... (remaining 63202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8061 Z= 0.193 Angle : 0.669 10.471 10947 Z= 0.341 Chirality : 0.274 4.959 1273 Planarity : 0.005 0.088 1359 Dihedral : 18.182 174.779 2987 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.35 % Allowed : 20.09 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.27), residues: 989 helix: 1.48 (0.20), residues: 703 sheet: -0.40 (0.78), residues: 36 loop : 1.26 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1442 TYR 0.008 0.001 TYR A 933 PHE 0.016 0.001 PHE A1057 TRP 0.047 0.001 TRP A1256 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8061) covalent geometry : angle 0.66934 (10947) hydrogen bonds : bond 0.15956 ( 533) hydrogen bonds : angle 6.34791 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 TRP cc_start: 0.7725 (m-90) cc_final: 0.7230 (m100) REVERT: A 1099 ARG cc_start: 0.7773 (mpt180) cc_final: 0.7106 (ttp80) REVERT: A 1138 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7464 (mt0) REVERT: A 1215 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6982 (ttm-80) REVERT: A 1225 ASN cc_start: 0.8196 (t0) cc_final: 0.7849 (t0) REVERT: A 1268 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7577 (ptpt) REVERT: A 1356 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 1386 GLU cc_start: 0.7889 (mp0) cc_final: 0.7589 (pm20) REVERT: A 1490 MET cc_start: 0.7099 (tpp) cc_final: 0.6721 (tpp) outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.1143 time to fit residues: 19.7989 Evaluate side-chains 113 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1356 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 961 ASN A1068 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.173813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129512 restraints weight = 10150.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128655 restraints weight = 6233.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129589 restraints weight = 4753.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129826 restraints weight = 4378.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130019 restraints weight = 4215.968| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8061 Z= 0.187 Angle : 0.626 11.054 10947 Z= 0.304 Chirality : 0.043 0.367 1273 Planarity : 0.004 0.045 1359 Dihedral : 7.623 58.826 1127 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.37 % Allowed : 19.28 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 989 helix: 1.78 (0.19), residues: 716 sheet: 1.30 (0.86), residues: 31 loop : 1.10 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1022 TYR 0.011 0.001 TYR A 933 PHE 0.017 0.002 PHE A 542 TRP 0.023 0.001 TRP A1256 HIS 0.004 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8061) covalent geometry : angle 0.62611 (10947) hydrogen bonds : bond 0.05213 ( 533) hydrogen bonds : angle 4.17014 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 TRP cc_start: 0.7712 (m-90) cc_final: 0.7053 (m100) REVERT: A 495 MET cc_start: 0.8416 (mmm) cc_final: 0.7888 (tpt) REVERT: A 773 ASP cc_start: 0.6747 (t0) cc_final: 0.6503 (t0) REVERT: A 1049 SER cc_start: 0.7645 (m) cc_final: 0.7192 (p) REVERT: A 1099 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7218 (ttp80) REVERT: A 1116 LYS cc_start: 0.7603 (pttm) cc_final: 0.7227 (tptt) REVERT: A 1215 ARG cc_start: 0.7310 (mtt180) cc_final: 0.7063 (ttm-80) REVERT: A 1356 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7702 (t0) REVERT: A 1386 GLU cc_start: 0.8159 (mp0) cc_final: 0.7869 (pm20) REVERT: A 1387 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8371 (mmtm) REVERT: A 1490 MET cc_start: 0.7454 (tpp) cc_final: 0.7223 (tpp) outliers start: 29 outliers final: 21 residues processed: 144 average time/residue: 0.0966 time to fit residues: 18.7798 Evaluate side-chains 131 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1350 GLU Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125438 restraints weight = 10126.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129355 restraints weight = 5731.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131788 restraints weight = 4088.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132990 restraints weight = 3369.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133718 restraints weight = 3025.120| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8061 Z= 0.143 Angle : 0.534 8.088 10947 Z= 0.264 Chirality : 0.040 0.265 1273 Planarity : 0.003 0.031 1359 Dihedral : 6.846 56.946 1127 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.48 % Allowed : 18.58 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.26), residues: 989 helix: 2.02 (0.19), residues: 715 sheet: 1.50 (0.88), residues: 31 loop : 1.04 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1442 TYR 0.009 0.001 TYR A 507 PHE 0.016 0.001 PHE A 342 TRP 0.035 0.001 TRP A1256 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8061) covalent geometry : angle 0.53393 (10947) hydrogen bonds : bond 0.04470 ( 533) hydrogen bonds : angle 3.77295 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 MET cc_start: 0.8257 (mmm) cc_final: 0.7904 (tpt) REVERT: A 519 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6821 (t) REVERT: A 1099 ARG cc_start: 0.8174 (mpt180) cc_final: 0.7531 (ttp80) REVERT: A 1116 LYS cc_start: 0.7605 (pttm) cc_final: 0.7338 (tptt) REVERT: A 1138 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7674 (mm-40) REVERT: A 1215 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6976 (ttm-80) REVERT: A 1356 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7543 (t0) REVERT: A 1490 MET cc_start: 0.7728 (tpp) cc_final: 0.7496 (tpp) outliers start: 30 outliers final: 18 residues processed: 142 average time/residue: 0.0832 time to fit residues: 16.3707 Evaluate side-chains 126 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.183733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139201 restraints weight = 10194.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139619 restraints weight = 6159.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140727 restraints weight = 4565.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141803 restraints weight = 3779.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141952 restraints weight = 3666.785| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8061 Z= 0.136 Angle : 0.543 9.507 10947 Z= 0.263 Chirality : 0.039 0.237 1273 Planarity : 0.003 0.029 1359 Dihedral : 6.457 55.689 1127 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.83 % Allowed : 19.28 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.26), residues: 989 helix: 2.11 (0.19), residues: 717 sheet: 0.43 (0.76), residues: 46 loop : 1.09 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1134 TYR 0.009 0.001 TYR A 507 PHE 0.013 0.001 PHE A 542 TRP 0.034 0.001 TRP A1256 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8061) covalent geometry : angle 0.54285 (10947) hydrogen bonds : bond 0.04248 ( 533) hydrogen bonds : angle 3.64918 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 MET cc_start: 0.8356 (mmm) cc_final: 0.7944 (tpt) REVERT: A 769 TYR cc_start: 0.7848 (m-80) cc_final: 0.7634 (m-80) REVERT: A 1099 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7621 (ttp80) REVERT: A 1116 LYS cc_start: 0.7753 (pttm) cc_final: 0.7518 (tptt) REVERT: A 1138 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7691 (mm-40) REVERT: A 1215 ARG cc_start: 0.7265 (mtt180) cc_final: 0.7032 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8133 (ptpt) cc_final: 0.7743 (ptpt) REVERT: A 1356 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7623 (t0) REVERT: A 1387 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8450 (mmmt) REVERT: A 1438 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7318 (tm-30) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.0863 time to fit residues: 16.4826 Evaluate side-chains 134 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1356 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 35 optimal weight: 0.0370 chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.183774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136463 restraints weight = 10084.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140720 restraints weight = 5373.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143389 restraints weight = 3709.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144704 restraints weight = 2980.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145680 restraints weight = 2646.493| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8061 Z= 0.130 Angle : 0.544 10.989 10947 Z= 0.263 Chirality : 0.039 0.232 1273 Planarity : 0.003 0.027 1359 Dihedral : 6.196 54.519 1127 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.41 % Allowed : 19.51 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.26), residues: 989 helix: 2.19 (0.19), residues: 719 sheet: 0.57 (0.76), residues: 46 loop : 1.05 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1134 TYR 0.009 0.001 TYR A 507 PHE 0.012 0.001 PHE A 542 TRP 0.036 0.001 TRP A1256 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8061) covalent geometry : angle 0.54432 (10947) hydrogen bonds : bond 0.04124 ( 533) hydrogen bonds : angle 3.60086 ( 1566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8386 (m-10) cc_final: 0.8008 (m-10) REVERT: A 485 MET cc_start: 0.8385 (tpp) cc_final: 0.8182 (tpt) REVERT: A 495 MET cc_start: 0.8251 (mmm) cc_final: 0.7841 (tpt) REVERT: A 519 CYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6883 (t) REVERT: A 1099 ARG cc_start: 0.8247 (mpt180) cc_final: 0.7611 (ttp80) REVERT: A 1138 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 1215 ARG cc_start: 0.7277 (mtt180) cc_final: 0.7025 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8069 (ptpt) cc_final: 0.7748 (ptpt) REVERT: A 1387 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8445 (mmmt) REVERT: A 1438 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7212 (tm-30) outliers start: 38 outliers final: 28 residues processed: 145 average time/residue: 0.0890 time to fit residues: 17.6949 Evaluate side-chains 140 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142621 restraints weight = 10115.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140541 restraints weight = 6360.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141328 restraints weight = 5162.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141679 restraints weight = 4803.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142550 restraints weight = 4409.954| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8061 Z= 0.137 Angle : 0.553 10.325 10947 Z= 0.265 Chirality : 0.039 0.216 1273 Planarity : 0.003 0.027 1359 Dihedral : 5.732 49.382 1125 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.07 % Allowed : 19.74 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.26), residues: 989 helix: 2.18 (0.19), residues: 720 sheet: 0.75 (0.76), residues: 46 loop : 0.91 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1134 TYR 0.009 0.001 TYR A 507 PHE 0.012 0.001 PHE A 542 TRP 0.040 0.001 TRP A1256 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8061) covalent geometry : angle 0.55317 (10947) hydrogen bonds : bond 0.04113 ( 533) hydrogen bonds : angle 3.62158 ( 1566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8322 (m-10) cc_final: 0.7919 (m-10) REVERT: A 485 MET cc_start: 0.8408 (tpp) cc_final: 0.8099 (tpt) REVERT: A 495 MET cc_start: 0.8384 (mmm) cc_final: 0.7938 (tpt) REVERT: A 519 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7037 (t) REVERT: A 1099 ARG cc_start: 0.8275 (mpt180) cc_final: 0.7787 (ttp80) REVERT: A 1138 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7712 (mm-40) REVERT: A 1205 TYR cc_start: 0.8634 (m-80) cc_final: 0.8430 (m-80) REVERT: A 1215 ARG cc_start: 0.7307 (mtt180) cc_final: 0.7102 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7762 (ptpt) REVERT: A 1387 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8542 (mmmt) REVERT: A 1438 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7208 (tm-30) outliers start: 35 outliers final: 31 residues processed: 144 average time/residue: 0.0968 time to fit residues: 18.8886 Evaluate side-chains 138 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132959 restraints weight = 10182.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137025 restraints weight = 5596.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139321 restraints weight = 3918.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140974 restraints weight = 3198.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141656 restraints weight = 2854.069| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8061 Z= 0.128 Angle : 0.553 13.150 10947 Z= 0.267 Chirality : 0.039 0.203 1273 Planarity : 0.003 0.032 1359 Dihedral : 5.564 50.119 1125 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.95 % Allowed : 20.09 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.27), residues: 989 helix: 2.25 (0.19), residues: 719 sheet: 0.93 (0.77), residues: 46 loop : 0.96 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1134 TYR 0.009 0.001 TYR A 507 PHE 0.011 0.001 PHE A 542 TRP 0.038 0.001 TRP A1256 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8061) covalent geometry : angle 0.55259 (10947) hydrogen bonds : bond 0.03992 ( 533) hydrogen bonds : angle 3.57625 ( 1566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8416 (m-10) cc_final: 0.7998 (m-10) REVERT: A 485 MET cc_start: 0.8392 (tpp) cc_final: 0.8070 (tpt) REVERT: A 495 MET cc_start: 0.8244 (mmm) cc_final: 0.7881 (tpt) REVERT: A 519 CYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6908 (t) REVERT: A 1099 ARG cc_start: 0.8324 (mpt180) cc_final: 0.7720 (ttp80) REVERT: A 1138 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7719 (mm-40) REVERT: A 1198 MET cc_start: 0.7206 (tpp) cc_final: 0.7001 (tpp) REVERT: A 1205 TYR cc_start: 0.8640 (m-80) cc_final: 0.8408 (m-80) REVERT: A 1215 ARG cc_start: 0.7290 (mtt180) cc_final: 0.7045 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7801 (ptpt) REVERT: A 1387 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8539 (mmmt) REVERT: A 1438 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7242 (tm-30) outliers start: 34 outliers final: 30 residues processed: 144 average time/residue: 0.0909 time to fit residues: 18.0670 Evaluate side-chains 138 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135455 restraints weight = 10148.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133835 restraints weight = 6368.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134048 restraints weight = 5528.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134306 restraints weight = 4937.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136798 restraints weight = 4521.060| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8061 Z= 0.160 Angle : 0.581 14.548 10947 Z= 0.282 Chirality : 0.040 0.181 1273 Planarity : 0.003 0.027 1359 Dihedral : 5.419 50.906 1125 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.07 % Allowed : 20.44 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 989 helix: 2.11 (0.19), residues: 719 sheet: 1.00 (0.78), residues: 46 loop : 0.85 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1134 TYR 0.010 0.001 TYR A 507 PHE 0.010 0.001 PHE A 542 TRP 0.039 0.001 TRP A1256 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8061) covalent geometry : angle 0.58111 (10947) hydrogen bonds : bond 0.04292 ( 533) hydrogen bonds : angle 3.68153 ( 1566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8389 (m-10) cc_final: 0.8002 (m-10) REVERT: A 485 MET cc_start: 0.8404 (tpp) cc_final: 0.8108 (tpt) REVERT: A 519 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6981 (t) REVERT: A 1095 MET cc_start: 0.8470 (mmm) cc_final: 0.8003 (mmp) REVERT: A 1099 ARG cc_start: 0.8332 (mpt180) cc_final: 0.7823 (ttp80) REVERT: A 1138 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7767 (mm-40) REVERT: A 1198 MET cc_start: 0.7249 (tpp) cc_final: 0.7048 (tpp) REVERT: A 1205 TYR cc_start: 0.8696 (m-80) cc_final: 0.8493 (m-80) REVERT: A 1215 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7163 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7821 (ptpt) REVERT: A 1387 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8542 (mmmt) REVERT: A 1438 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7275 (tm-30) outliers start: 35 outliers final: 33 residues processed: 142 average time/residue: 0.0860 time to fit residues: 16.9970 Evaluate side-chains 143 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1152 CYS Chi-restraints excluded: chain A residue 1225 ASN Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.180295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139026 restraints weight = 10024.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138085 restraints weight = 5980.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138573 restraints weight = 4773.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.138879 restraints weight = 4318.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139376 restraints weight = 4146.832| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8061 Z= 0.116 Angle : 0.538 14.328 10947 Z= 0.262 Chirality : 0.038 0.177 1273 Planarity : 0.003 0.032 1359 Dihedral : 5.237 51.207 1125 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.90 % Allowed : 21.25 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.27), residues: 989 helix: 2.33 (0.19), residues: 718 sheet: 1.07 (0.77), residues: 46 loop : 0.94 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1134 TYR 0.008 0.001 TYR A 507 PHE 0.011 0.001 PHE A 542 TRP 0.047 0.001 TRP A1256 HIS 0.001 0.000 HIS A1333 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8061) covalent geometry : angle 0.53796 (10947) hydrogen bonds : bond 0.03816 ( 533) hydrogen bonds : angle 3.56111 ( 1566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8418 (m-10) cc_final: 0.8054 (m-10) REVERT: A 495 MET cc_start: 0.8275 (mmm) cc_final: 0.7893 (tpt) REVERT: A 519 CYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 1095 MET cc_start: 0.8426 (mmm) cc_final: 0.7917 (mmp) REVERT: A 1099 ARG cc_start: 0.8306 (mpt180) cc_final: 0.7776 (ttp80) REVERT: A 1116 LYS cc_start: 0.8154 (tptt) cc_final: 0.7933 (tptp) REVERT: A 1138 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7759 (mm-40) REVERT: A 1198 MET cc_start: 0.7228 (tpp) cc_final: 0.7022 (tpp) REVERT: A 1215 ARG cc_start: 0.7300 (mtt180) cc_final: 0.7052 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7827 (ptpt) REVERT: A 1350 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7405 (mm-30) REVERT: A 1387 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8537 (mmmt) outliers start: 25 outliers final: 23 residues processed: 134 average time/residue: 0.0849 time to fit residues: 15.7238 Evaluate side-chains 135 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 83 optimal weight: 0.0060 chunk 6 optimal weight: 0.4980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.182212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138405 restraints weight = 10105.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138767 restraints weight = 5936.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139648 restraints weight = 4494.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139768 restraints weight = 3887.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141609 restraints weight = 3790.291| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 8061 Z= 0.112 Angle : 0.539 14.320 10947 Z= 0.261 Chirality : 0.038 0.191 1273 Planarity : 0.003 0.034 1359 Dihedral : 5.143 52.171 1125 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.90 % Allowed : 21.60 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.27), residues: 989 helix: 2.41 (0.19), residues: 718 sheet: 1.11 (0.77), residues: 46 loop : 0.97 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1134 TYR 0.008 0.001 TYR A 507 PHE 0.011 0.001 PHE A 542 TRP 0.044 0.001 TRP A1256 HIS 0.001 0.000 HIS A1333 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8061) covalent geometry : angle 0.53908 (10947) hydrogen bonds : bond 0.03713 ( 533) hydrogen bonds : angle 3.55910 ( 1566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 TYR cc_start: 0.8414 (m-10) cc_final: 0.8070 (m-10) REVERT: A 481 LYS cc_start: 0.8652 (tmmt) cc_final: 0.8358 (ttmt) REVERT: A 495 MET cc_start: 0.8236 (mmm) cc_final: 0.7856 (tpt) REVERT: A 519 CYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6877 (t) REVERT: A 1099 ARG cc_start: 0.8301 (mpt180) cc_final: 0.7756 (ttp80) REVERT: A 1138 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7956 (mm-40) REVERT: A 1215 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7044 (ttm-80) REVERT: A 1268 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7798 (ptpt) REVERT: A 1350 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 1387 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8545 (mmmt) outliers start: 25 outliers final: 21 residues processed: 139 average time/residue: 0.0893 time to fit residues: 16.9750 Evaluate side-chains 135 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 519 CYS Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1235 GLN Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.183416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140061 restraints weight = 10250.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139430 restraints weight = 5850.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139303 restraints weight = 4844.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140688 restraints weight = 5350.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140543 restraints weight = 4151.643| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8061 Z= 0.132 Angle : 0.564 15.397 10947 Z= 0.276 Chirality : 0.039 0.238 1273 Planarity : 0.003 0.034 1359 Dihedral : 5.143 53.109 1125 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.14 % Allowed : 21.37 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.27), residues: 989 helix: 2.33 (0.19), residues: 718 sheet: 1.12 (0.77), residues: 46 loop : 0.95 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1134 TYR 0.009 0.001 TYR A1100 PHE 0.010 0.001 PHE A 542 TRP 0.044 0.001 TRP A1256 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8061) covalent geometry : angle 0.56397 (10947) hydrogen bonds : bond 0.03873 ( 533) hydrogen bonds : angle 3.62083 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.29 seconds wall clock time: 25 minutes 43.88 seconds (1543.88 seconds total)