Starting phenix.real_space_refine on Sat Jun 14 14:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.map" model { file = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3a_62011/06_2025/9k3a_62011.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 10107 2.51 5 N 2851 2.21 5 O 3116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7756 Classifications: {'peptide': 973} Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 936} Chain breaks: 6 Chain: "B" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8366 Classifications: {'peptide': 1071} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 72, 'TRANS': 997} Chain breaks: 10 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.06, per 1000 atoms: 0.56 Number of scatterers: 16122 At special positions: 0 Unit cell: (193.67, 138.03, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3116 8.00 N 2851 7.00 C 10107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS B1715 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.2 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3868 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 12 sheets defined 59.9% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.609A pdb=" N SER A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 removed outlier: 3.517A pdb=" N LEU A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.671A pdb=" N LEU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 157 removed outlier: 3.502A pdb=" N VAL A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 177 Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 189 through 211 Processing helix chain 'A' and resid 213 through 229 Processing helix chain 'A' and resid 229 through 241 Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.835A pdb=" N VAL A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.911A pdb=" N LEU A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 332 through 343 Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 365 through 376 removed outlier: 3.575A pdb=" N PHE A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.906A pdb=" N ASN A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.980A pdb=" N LYS A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 455 through 463 removed outlier: 3.572A pdb=" N ALA A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 482 removed outlier: 3.564A pdb=" N SER A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 504 removed outlier: 4.049A pdb=" N LYS A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 510 removed outlier: 3.524A pdb=" N ARG A 510 " --> pdb=" O LEU A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 511 through 530 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.588A pdb=" N SER A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 3.762A pdb=" N GLY A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 612 removed outlier: 4.374A pdb=" N GLY A 609 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 631 removed outlier: 3.534A pdb=" N ALA A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.953A pdb=" N TYR A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 679 Processing helix chain 'A' and resid 683 through 696 removed outlier: 3.905A pdb=" N LEU A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'A' and resid 731 through 739 removed outlier: 3.711A pdb=" N ILE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.631A pdb=" N GLN A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 761 through 772 removed outlier: 4.488A pdb=" N TYR A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA A 768 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 790 removed outlier: 4.266A pdb=" N LEU A 789 " --> pdb=" O ASN A 785 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 790 " --> pdb=" O GLN A 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 790' Processing helix chain 'A' and resid 810 through 813 removed outlier: 4.529A pdb=" N GLY A 813 " --> pdb=" O ASP A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 865 through 874 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 970 through 975 Processing helix chain 'A' and resid 981 through 987 Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.587A pdb=" N THR A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1028 removed outlier: 3.562A pdb=" N ARG A1024 " --> pdb=" O VAL A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1070 Processing helix chain 'A' and resid 1072 through 1083 removed outlier: 4.550A pdb=" N GLN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1090 removed outlier: 3.841A pdb=" N ASP A1089 " --> pdb=" O ASN A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 4.242A pdb=" N GLU A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A1112 " --> pdb=" O ARG A1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.717A pdb=" N ILE B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.577A pdb=" N ARG B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.512A pdb=" N PHE B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.680A pdb=" N VAL B 608 " --> pdb=" O PRO B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 633 Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.629A pdb=" N LEU B 639 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 884 Processing helix chain 'B' and resid 896 through 899 Processing helix chain 'B' and resid 908 through 916 Processing helix chain 'B' and resid 932 through 957 Processing helix chain 'B' and resid 959 through 979 removed outlier: 3.733A pdb=" N ALA B 978 " --> pdb=" O ARG B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1025 through 1029 Processing helix chain 'B' and resid 1035 through 1046 Processing helix chain 'B' and resid 1074 through 1083 Processing helix chain 'B' and resid 1087 through 1094 Processing helix chain 'B' and resid 1102 through 1108 Processing helix chain 'B' and resid 1151 through 1165 Processing helix chain 'B' and resid 1166 through 1168 No H-bonds generated for 'chain 'B' and resid 1166 through 1168' Processing helix chain 'B' and resid 1175 through 1188 Processing helix chain 'B' and resid 1193 through 1204 Processing helix chain 'B' and resid 1206 through 1210 Processing helix chain 'B' and resid 1213 through 1259 Processing helix chain 'B' and resid 1452 through 1462 Processing helix chain 'B' and resid 1465 through 1470 removed outlier: 3.743A pdb=" N GLU B1470 " --> pdb=" O PRO B1466 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1513 Processing helix chain 'B' and resid 1514 through 1526 Processing helix chain 'B' and resid 1539 through 1554 Processing helix chain 'B' and resid 1559 through 1578 Processing helix chain 'B' and resid 1592 through 1594 No H-bonds generated for 'chain 'B' and resid 1592 through 1594' Processing helix chain 'B' and resid 1608 through 1627 Processing helix chain 'B' and resid 1630 through 1707 removed outlier: 3.675A pdb=" N ASN B1634 " --> pdb=" O ILE B1630 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 568 removed outlier: 3.911A pdb=" N GLU A 566 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 681 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 803 Processing sheet with id=AA4, first strand: chain 'A' and resid 823 through 824 Processing sheet with id=AA5, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 470 removed outlier: 3.833A pdb=" N ARG B 717 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 856 through 860 removed outlier: 3.513A pdb=" N ARG B 857 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 919 through 921 Processing sheet with id=AA9, first strand: chain 'B' and resid 996 through 998 removed outlier: 6.472A pdb=" N ARG B1125 " --> pdb=" O LEU B1115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1032 through 1033 Processing sheet with id=AB2, first strand: chain 'B' and resid 1424 through 1430 removed outlier: 5.656A pdb=" N VAL B1430 " --> pdb=" O GLN B1477 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLN B1477 " --> pdb=" O VAL B1430 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN B1600 " --> pdb=" O GLU B1482 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B1484 " --> pdb=" O VAL B1598 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1598 " --> pdb=" O LEU B1484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1447 through 1450 876 hydrogen bonds defined for protein. 2562 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: 6.07 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 6860 1.44 - 1.65: 9452 1.65 - 1.87: 95 1.87 - 2.09: 0 2.09 - 2.31: 1 Bond restraints: 16408 Sorted by residual: bond pdb=" N PRO B 599 " pdb=" CD PRO B 599 " ideal model delta sigma weight residual 1.473 2.310 -0.837 1.40e-02 5.10e+03 3.57e+03 bond pdb=" N PRO B 472 " pdb=" CA PRO B 472 " ideal model delta sigma weight residual 1.472 1.367 0.105 1.34e-02 5.57e+03 6.13e+01 bond pdb=" N SER A 702 " pdb=" CA SER A 702 " ideal model delta sigma weight residual 1.458 1.532 -0.074 1.33e-02 5.65e+03 3.13e+01 bond pdb=" N GLY B 474 " pdb=" CA GLY B 474 " ideal model delta sigma weight residual 1.449 1.524 -0.075 1.45e-02 4.76e+03 2.69e+01 bond pdb=" C PRO A 700 " pdb=" N ILE A 701 " ideal model delta sigma weight residual 1.329 1.392 -0.062 1.22e-02 6.72e+03 2.59e+01 ... (remaining 16403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.05: 22190 11.05 - 22.11: 21 22.11 - 33.16: 7 33.16 - 44.22: 2 44.22 - 55.27: 1 Bond angle restraints: 22221 Sorted by residual: angle pdb=" N THR B 359 " pdb=" CA THR B 359 " pdb=" C THR B 359 " ideal model delta sigma weight residual 111.87 167.14 -55.27 1.41e+00 5.03e-01 1.54e+03 angle pdb=" CA PRO B 599 " pdb=" N PRO B 599 " pdb=" CD PRO B 599 " ideal model delta sigma weight residual 112.00 75.90 36.10 1.40e+00 5.10e-01 6.65e+02 angle pdb=" N GLY B 481 " pdb=" CA GLY B 481 " pdb=" C GLY B 481 " ideal model delta sigma weight residual 111.18 78.47 32.71 1.54e+00 4.22e-01 4.51e+02 angle pdb=" C ASP B1584 " pdb=" CA ASP B1584 " pdb=" CB ASP B1584 " ideal model delta sigma weight residual 111.48 148.66 -37.18 1.91e+00 2.74e-01 3.79e+02 angle pdb=" N PRO B 599 " pdb=" CD PRO B 599 " pdb=" CG PRO B 599 " ideal model delta sigma weight residual 103.20 75.50 27.70 1.50e+00 4.44e-01 3.41e+02 ... (remaining 22216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8733 17.98 - 35.96: 1089 35.96 - 53.95: 222 53.95 - 71.93: 39 71.93 - 89.91: 17 Dihedral angle restraints: 10100 sinusoidal: 4153 harmonic: 5947 Sorted by residual: dihedral pdb=" N THR B 359 " pdb=" C THR B 359 " pdb=" CA THR B 359 " pdb=" CB THR B 359 " ideal model delta harmonic sigma weight residual 123.40 83.48 39.92 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C ASN B 357 " pdb=" N ASN B 357 " pdb=" CA ASN B 357 " pdb=" CB ASN B 357 " ideal model delta harmonic sigma weight residual -122.60 -161.65 39.05 0 2.50e+00 1.60e-01 2.44e+02 dihedral pdb=" C THR B 359 " pdb=" N THR B 359 " pdb=" CA THR B 359 " pdb=" CB THR B 359 " ideal model delta harmonic sigma weight residual -122.00 -83.31 -38.69 0 2.50e+00 1.60e-01 2.40e+02 ... (remaining 10097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 2496 0.353 - 0.706: 5 0.706 - 1.059: 3 1.059 - 1.413: 0 1.413 - 1.766: 2 Chirality restraints: 2506 Sorted by residual: chirality pdb=" CA THR B 359 " pdb=" N THR B 359 " pdb=" C THR B 359 " pdb=" CB THR B 359 " both_signs ideal model delta sigma weight residual False 2.53 0.76 1.77 2.00e-01 2.50e+01 7.79e+01 chirality pdb=" CA ASN B 357 " pdb=" N ASN B 357 " pdb=" C ASN B 357 " pdb=" CB ASN B 357 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.06e+01 chirality pdb=" CA ASP B1584 " pdb=" N ASP B1584 " pdb=" C ASP B1584 " pdb=" CB ASP B1584 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 2503 not shown) Planarity restraints: 2908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 703 " 0.850 9.50e-02 1.11e+02 3.81e-01 8.81e+01 pdb=" NE ARG A 703 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG A 703 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 703 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 703 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 598 " 0.185 5.00e-02 4.00e+02 2.05e-01 6.75e+01 pdb=" N PRO B 599 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 700 " -0.026 2.00e-02 2.50e+03 5.61e-02 3.14e+01 pdb=" C PRO A 700 " 0.097 2.00e-02 2.50e+03 pdb=" O PRO A 700 " -0.038 2.00e-02 2.50e+03 pdb=" N ILE A 701 " -0.032 2.00e-02 2.50e+03 ... (remaining 2905 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 64 2.38 - 3.01: 9267 3.01 - 3.64: 23873 3.64 - 4.27: 34646 4.27 - 4.90: 58635 Nonbonded interactions: 126485 Sorted by model distance: nonbonded pdb=" O ILE A 704 " pdb=" CG2 ILE A 704 " model vdw 1.754 3.460 nonbonded pdb=" OD2 ASP B 638 " pdb=" NH2 ARG B 717 " model vdw 1.781 3.120 nonbonded pdb=" CB THR B 471 " pdb=" O LYS B 473 " model vdw 1.812 3.470 nonbonded pdb=" N GLY B 481 " pdb=" O GLY B 481 " model vdw 1.853 2.496 nonbonded pdb=" N LYS B 358 " pdb=" O LYS B 358 " model vdw 2.009 2.496 ... (remaining 126480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 38.370 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.008 0.837 16409 Z= 0.523 Angle : 1.108 55.270 22223 Z= 0.699 Chirality : 0.077 1.766 2506 Planarity : 0.011 0.381 2908 Dihedral : 16.141 89.910 6229 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.40 % Allowed : 16.72 % Favored : 82.88 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 2008 helix: 2.17 (0.16), residues: 1103 sheet: -0.18 (0.55), residues: 96 loop : -1.14 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 424 HIS 0.008 0.001 HIS A 717 PHE 0.035 0.002 PHE A 742 TYR 0.014 0.001 TYR A 380 ARG 0.020 0.001 ARG A1083 Details of bonding type rmsd hydrogen bonds : bond 0.14361 ( 876) hydrogen bonds : angle 5.25235 ( 2562) SS BOND : bond 0.00489 ( 1) SS BOND : angle 1.59749 ( 2) covalent geometry : bond 0.00790 (16408) covalent geometry : angle 1.10775 (22221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 407 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8596 (t70) cc_final: 0.8243 (t0) outliers start: 7 outliers final: 5 residues processed: 411 average time/residue: 0.3233 time to fit residues: 193.7838 Evaluate side-chains 405 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 400 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 1508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 159 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 185 optimal weight: 0.0570 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN A 786 GLN A 812 ASN A 979 ASN A1029 ASN A1100 GLN B 187 GLN B 194 ASN B 233 GLN B 348 ASN B 496 ASN B 716 GLN B1131 ASN ** B1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1437 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.167824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.127435 restraints weight = 19593.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.127799 restraints weight = 14181.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128651 restraints weight = 15203.604| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16409 Z= 0.150 Angle : 0.583 13.251 22223 Z= 0.297 Chirality : 0.041 0.229 2506 Planarity : 0.006 0.081 2908 Dihedral : 4.805 82.694 2222 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.49 % Allowed : 16.16 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 2008 helix: 2.20 (0.15), residues: 1136 sheet: -0.29 (0.60), residues: 82 loop : -1.11 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 424 HIS 0.005 0.001 HIS A 40 PHE 0.024 0.001 PHE A 742 TYR 0.015 0.001 TYR B1425 ARG 0.010 0.001 ARG A 476 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 876) hydrogen bonds : angle 4.21390 ( 2562) SS BOND : bond 0.00376 ( 1) SS BOND : angle 1.38666 ( 2) covalent geometry : bond 0.00354 (16408) covalent geometry : angle 0.58297 (22221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8614 (t70) cc_final: 0.8271 (t0) REVERT: A 328 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 639 LYS cc_start: 0.7982 (tppt) cc_final: 0.7572 (tppt) REVERT: A 740 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6966 (ttm110) REVERT: A 874 PHE cc_start: 0.8403 (m-80) cc_final: 0.8146 (m-80) REVERT: B 899 MET cc_start: 0.8296 (tmm) cc_final: 0.8002 (ppp) REVERT: B 1181 GLU cc_start: 0.7152 (pt0) cc_final: 0.6748 (pt0) REVERT: B 1584 ASP cc_start: 0.8402 (p0) cc_final: 0.8109 (p0) REVERT: B 1658 ASP cc_start: 0.7733 (t0) cc_final: 0.7464 (t0) outliers start: 44 outliers final: 29 residues processed: 439 average time/residue: 0.2993 time to fit residues: 191.2206 Evaluate side-chains 416 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 387 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1442 GLU Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1497 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN A 538 HIS B 187 GLN B 194 ASN B 222 ASN B 348 ASN B 998 ASN B1602 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.170330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130570 restraints weight = 19767.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130365 restraints weight = 12487.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.130574 restraints weight = 14494.898| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16409 Z= 0.192 Angle : 0.593 12.780 22223 Z= 0.297 Chirality : 0.042 0.172 2506 Planarity : 0.005 0.089 2908 Dihedral : 4.711 88.043 2218 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.29 % Allowed : 16.95 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.19), residues: 2008 helix: 2.18 (0.15), residues: 1129 sheet: -0.45 (0.55), residues: 92 loop : -1.09 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 424 HIS 0.006 0.001 HIS A 40 PHE 0.016 0.001 PHE A 742 TYR 0.015 0.002 TYR B 466 ARG 0.010 0.001 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 876) hydrogen bonds : angle 4.14793 ( 2562) SS BOND : bond 0.00371 ( 1) SS BOND : angle 1.18398 ( 2) covalent geometry : bond 0.00463 (16408) covalent geometry : angle 0.59253 (22221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 417 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8628 (t70) cc_final: 0.8357 (t70) REVERT: A 328 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 518 ASN cc_start: 0.8644 (m-40) cc_final: 0.8252 (m110) REVERT: A 639 LYS cc_start: 0.8139 (tppt) cc_final: 0.7622 (tppt) REVERT: B 509 ARG cc_start: 0.6535 (ttm-80) cc_final: 0.6204 (mtp85) REVERT: B 881 ASP cc_start: 0.7506 (m-30) cc_final: 0.7251 (m-30) REVERT: B 1104 ASP cc_start: 0.8453 (m-30) cc_final: 0.8238 (m-30) REVERT: B 1116 ASP cc_start: 0.7620 (t0) cc_final: 0.7202 (t0) REVERT: B 1121 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 1181 GLU cc_start: 0.7266 (pt0) cc_final: 0.6851 (pt0) REVERT: B 1492 ASP cc_start: 0.7899 (t0) cc_final: 0.7698 (t70) outliers start: 58 outliers final: 34 residues processed: 448 average time/residue: 0.3155 time to fit residues: 206.0878 Evaluate side-chains 440 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 405 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1506 LEU Chi-restraints excluded: chain B residue 1525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 136 optimal weight: 0.0170 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS B 194 ASN B 892 ASN B 998 ASN B1131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.173245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132675 restraints weight = 19778.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.132508 restraints weight = 13668.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.132937 restraints weight = 12588.205| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16409 Z= 0.120 Angle : 0.539 11.255 22223 Z= 0.271 Chirality : 0.040 0.215 2506 Planarity : 0.005 0.078 2908 Dihedral : 4.532 89.288 2218 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.83 % Allowed : 18.03 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.19), residues: 2008 helix: 2.35 (0.15), residues: 1128 sheet: -0.52 (0.51), residues: 103 loop : -0.95 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.004 0.001 HIS A 717 PHE 0.015 0.001 PHE A 742 TYR 0.021 0.001 TYR B 466 ARG 0.010 0.000 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 876) hydrogen bonds : angle 3.92224 ( 2562) SS BOND : bond 0.00397 ( 1) SS BOND : angle 1.03680 ( 2) covalent geometry : bond 0.00277 (16408) covalent geometry : angle 0.53916 (22221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 414 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8628 (t70) cc_final: 0.8297 (t0) REVERT: A 156 MET cc_start: 0.7665 (tpp) cc_final: 0.7425 (tmm) REVERT: A 438 GLU cc_start: 0.7467 (mp0) cc_final: 0.7236 (mp0) REVERT: A 518 ASN cc_start: 0.8555 (m-40) cc_final: 0.8093 (m110) REVERT: A 527 ASN cc_start: 0.8759 (t0) cc_final: 0.8537 (t0) REVERT: A 639 LYS cc_start: 0.8198 (tppt) cc_final: 0.7716 (tppt) REVERT: A 747 MET cc_start: 0.8220 (tpp) cc_final: 0.7895 (tpp) REVERT: B 509 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6197 (mtp85) REVERT: B 881 ASP cc_start: 0.7531 (m-30) cc_final: 0.7260 (m-30) REVERT: B 1104 ASP cc_start: 0.8464 (m-30) cc_final: 0.8229 (m-30) REVERT: B 1116 ASP cc_start: 0.7628 (t0) cc_final: 0.7125 (t0) REVERT: B 1121 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: B 1177 GLU cc_start: 0.6612 (pp20) cc_final: 0.5961 (pp20) REVERT: B 1181 GLU cc_start: 0.7290 (pt0) cc_final: 0.6205 (pt0) REVERT: B 1253 ASP cc_start: 0.8563 (t0) cc_final: 0.7781 (m-30) outliers start: 50 outliers final: 34 residues processed: 443 average time/residue: 0.3062 time to fit residues: 199.3266 Evaluate side-chains 432 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 397 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 100 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 163 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 overall best weight: 3.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN B 187 GLN B 194 ASN B 222 ASN ** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.164243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124309 restraints weight = 20178.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123767 restraints weight = 13146.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124310 restraints weight = 15373.067| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16409 Z= 0.223 Angle : 0.613 12.377 22223 Z= 0.305 Chirality : 0.043 0.190 2506 Planarity : 0.005 0.101 2908 Dihedral : 4.512 78.060 2217 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.23 % Allowed : 19.22 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2008 helix: 2.21 (0.15), residues: 1125 sheet: -0.66 (0.53), residues: 93 loop : -1.03 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 711 HIS 0.007 0.001 HIS A 40 PHE 0.014 0.001 PHE A 369 TYR 0.016 0.002 TYR B 466 ARG 0.011 0.001 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 876) hydrogen bonds : angle 4.11155 ( 2562) SS BOND : bond 0.00373 ( 1) SS BOND : angle 1.07943 ( 2) covalent geometry : bond 0.00536 (16408) covalent geometry : angle 0.61342 (22221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 418 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8640 (t70) cc_final: 0.8382 (t70) REVERT: A 161 MET cc_start: 0.8268 (pmm) cc_final: 0.7612 (pmm) REVERT: A 338 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 397 GLU cc_start: 0.8495 (tp30) cc_final: 0.8203 (tm-30) REVERT: A 510 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7042 (mmp-170) REVERT: A 518 ASN cc_start: 0.8550 (m-40) cc_final: 0.8128 (m110) REVERT: A 527 ASN cc_start: 0.8940 (t0) cc_final: 0.8466 (t0) REVERT: A 628 SER cc_start: 0.8254 (m) cc_final: 0.7990 (p) REVERT: A 639 LYS cc_start: 0.8169 (tppt) cc_final: 0.7651 (tppt) REVERT: A 671 TYR cc_start: 0.9129 (m-80) cc_final: 0.8612 (m-80) REVERT: B 509 ARG cc_start: 0.6631 (ttm-80) cc_final: 0.6221 (mtp85) REVERT: B 616 PHE cc_start: 0.6648 (m-80) cc_final: 0.6439 (m-80) REVERT: B 717 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7614 (mtp-110) REVERT: B 879 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8906 (tt) REVERT: B 881 ASP cc_start: 0.7498 (m-30) cc_final: 0.7264 (m-30) REVERT: B 899 MET cc_start: 0.8284 (tmm) cc_final: 0.7986 (ppp) REVERT: B 917 ASP cc_start: 0.7634 (t0) cc_final: 0.7277 (t0) REVERT: B 1116 ASP cc_start: 0.7733 (t0) cc_final: 0.7196 (t0) REVERT: B 1121 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: B 1156 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8141 (ttp-110) REVERT: B 1181 GLU cc_start: 0.7339 (pt0) cc_final: 0.6953 (pt0) REVERT: B 1522 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8566 (mtpt) outliers start: 57 outliers final: 38 residues processed: 449 average time/residue: 0.3084 time to fit residues: 202.2845 Evaluate side-chains 436 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 396 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 840 VAL Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS A 841 ASN B 194 ASN B1131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.168109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.127072 restraints weight = 20016.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127462 restraints weight = 13588.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.127666 restraints weight = 12767.325| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16409 Z= 0.142 Angle : 0.562 11.524 22223 Z= 0.279 Chirality : 0.041 0.327 2506 Planarity : 0.005 0.080 2908 Dihedral : 4.326 68.975 2216 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.00 % Allowed : 19.56 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2008 helix: 2.35 (0.15), residues: 1124 sheet: -0.68 (0.53), residues: 93 loop : -0.94 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 711 HIS 0.005 0.001 HIS A 468 PHE 0.013 0.001 PHE A 742 TYR 0.022 0.001 TYR A 546 ARG 0.006 0.000 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 876) hydrogen bonds : angle 3.92350 ( 2562) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.97688 ( 2) covalent geometry : bond 0.00337 (16408) covalent geometry : angle 0.56156 (22221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 404 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8672 (t70) cc_final: 0.8318 (t0) REVERT: A 438 GLU cc_start: 0.7539 (mp0) cc_final: 0.7220 (mp0) REVERT: A 518 ASN cc_start: 0.8538 (m-40) cc_final: 0.8091 (m110) REVERT: A 527 ASN cc_start: 0.8787 (t0) cc_final: 0.8347 (t0) REVERT: A 628 SER cc_start: 0.8246 (m) cc_final: 0.7969 (p) REVERT: A 639 LYS cc_start: 0.8196 (tppt) cc_final: 0.7652 (tppt) REVERT: A 747 MET cc_start: 0.8265 (tpp) cc_final: 0.7974 (tpp) REVERT: B 509 ARG cc_start: 0.6663 (ttm-80) cc_final: 0.6168 (mtp85) REVERT: B 598 ASN cc_start: 0.8583 (m-40) cc_final: 0.8229 (m-40) REVERT: B 646 ASP cc_start: 0.7693 (p0) cc_final: 0.7425 (p0) REVERT: B 704 ASP cc_start: 0.8669 (t70) cc_final: 0.8401 (t0) REVERT: B 879 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8887 (tt) REVERT: B 881 ASP cc_start: 0.7572 (m-30) cc_final: 0.7284 (m-30) REVERT: B 1104 ASP cc_start: 0.8457 (m-30) cc_final: 0.8172 (m-30) REVERT: B 1116 ASP cc_start: 0.7701 (t0) cc_final: 0.7142 (t0) REVERT: B 1121 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: B 1181 GLU cc_start: 0.7390 (pt0) cc_final: 0.7068 (pt0) REVERT: B 1253 ASP cc_start: 0.8567 (t0) cc_final: 0.7765 (m-30) REVERT: B 1492 ASP cc_start: 0.7973 (t0) cc_final: 0.7762 (t70) REVERT: B 1522 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8613 (mtpt) outliers start: 53 outliers final: 38 residues processed: 433 average time/residue: 0.3098 time to fit residues: 196.1201 Evaluate side-chains 430 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 194 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 0.0470 chunk 181 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN B 194 ASN ** B 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 ASN B1131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.170527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131213 restraints weight = 20030.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.129130 restraints weight = 15222.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.131130 restraints weight = 13928.691| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16409 Z= 0.127 Angle : 0.555 10.771 22223 Z= 0.274 Chirality : 0.040 0.274 2506 Planarity : 0.005 0.090 2908 Dihedral : 4.182 59.879 2216 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.89 % Allowed : 19.61 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 2008 helix: 2.47 (0.15), residues: 1116 sheet: -0.70 (0.49), residues: 103 loop : -0.83 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 711 HIS 0.005 0.001 HIS A 717 PHE 0.028 0.001 PHE A 742 TYR 0.017 0.001 TYR A 546 ARG 0.007 0.000 ARG B 717 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 876) hydrogen bonds : angle 3.82694 ( 2562) SS BOND : bond 0.00416 ( 1) SS BOND : angle 0.93733 ( 2) covalent geometry : bond 0.00296 (16408) covalent geometry : angle 0.55466 (22221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8657 (t70) cc_final: 0.8256 (t0) REVERT: A 338 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 518 ASN cc_start: 0.8577 (m-40) cc_final: 0.8131 (m110) REVERT: A 527 ASN cc_start: 0.8725 (t0) cc_final: 0.8411 (t0) REVERT: A 549 LYS cc_start: 0.8662 (mmpt) cc_final: 0.8097 (mmpt) REVERT: A 639 LYS cc_start: 0.8216 (tppt) cc_final: 0.7792 (tppt) REVERT: B 509 ARG cc_start: 0.6559 (ttm-80) cc_final: 0.6115 (mtp85) REVERT: B 598 ASN cc_start: 0.8630 (m-40) cc_final: 0.8149 (m-40) REVERT: B 879 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8889 (tt) REVERT: B 881 ASP cc_start: 0.7459 (m-30) cc_final: 0.7190 (m-30) REVERT: B 899 MET cc_start: 0.8148 (tmm) cc_final: 0.7828 (ppp) REVERT: B 1065 ARG cc_start: 0.8619 (ptp-170) cc_final: 0.8275 (mtt180) REVERT: B 1078 TYR cc_start: 0.9363 (t80) cc_final: 0.9156 (t80) REVERT: B 1116 ASP cc_start: 0.7655 (t0) cc_final: 0.7106 (t0) REVERT: B 1121 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: B 1181 GLU cc_start: 0.7322 (pt0) cc_final: 0.7014 (pt0) REVERT: B 1253 ASP cc_start: 0.8570 (t0) cc_final: 0.7785 (m-30) REVERT: B 1522 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8623 (mtpt) outliers start: 51 outliers final: 37 residues processed: 433 average time/residue: 0.3176 time to fit residues: 201.3007 Evaluate side-chains 425 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 386 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 0.0070 chunk 154 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 108 optimal weight: 0.6980 overall best weight: 0.9378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS A 841 ASN B 187 GLN B 194 ASN B1131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.172869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131811 restraints weight = 19911.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133005 restraints weight = 13668.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133312 restraints weight = 12573.426| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16409 Z= 0.116 Angle : 0.551 10.382 22223 Z= 0.273 Chirality : 0.040 0.259 2506 Planarity : 0.005 0.077 2908 Dihedral : 4.098 53.839 2216 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.61 % Allowed : 20.18 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 2008 helix: 2.55 (0.15), residues: 1112 sheet: -0.64 (0.49), residues: 103 loop : -0.76 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 711 HIS 0.005 0.001 HIS A 717 PHE 0.026 0.001 PHE A 742 TYR 0.014 0.001 TYR A 546 ARG 0.008 0.000 ARG A 999 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 876) hydrogen bonds : angle 3.76191 ( 2562) SS BOND : bond 0.00419 ( 1) SS BOND : angle 0.86603 ( 2) covalent geometry : bond 0.00267 (16408) covalent geometry : angle 0.55107 (22221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 395 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8658 (t70) cc_final: 0.8244 (t0) REVERT: A 438 GLU cc_start: 0.7604 (mp0) cc_final: 0.7348 (mp0) REVERT: A 518 ASN cc_start: 0.8580 (m-40) cc_final: 0.8093 (m110) REVERT: A 527 ASN cc_start: 0.8666 (t0) cc_final: 0.8396 (t0) REVERT: A 549 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8101 (mmpt) REVERT: A 639 LYS cc_start: 0.8176 (tppt) cc_final: 0.7757 (tppt) REVERT: A 747 MET cc_start: 0.8235 (tpp) cc_final: 0.7900 (tpp) REVERT: A 834 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 999 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8074 (ttp80) REVERT: A 1047 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 509 ARG cc_start: 0.6527 (ttm-80) cc_final: 0.6105 (mtp85) REVERT: B 598 ASN cc_start: 0.8618 (m-40) cc_final: 0.8242 (m-40) REVERT: B 879 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8833 (tt) REVERT: B 881 ASP cc_start: 0.7477 (m-30) cc_final: 0.7192 (m-30) REVERT: B 899 MET cc_start: 0.8196 (tmm) cc_final: 0.7865 (ppp) REVERT: B 1078 TYR cc_start: 0.9349 (t80) cc_final: 0.9115 (t80) REVERT: B 1116 ASP cc_start: 0.7636 (t0) cc_final: 0.7088 (t0) REVERT: B 1121 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: B 1181 GLU cc_start: 0.7244 (pt0) cc_final: 0.6935 (pt0) REVERT: B 1425 TYR cc_start: 0.8817 (m-80) cc_final: 0.8552 (m-80) REVERT: B 1522 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8600 (mtpt) outliers start: 46 outliers final: 38 residues processed: 422 average time/residue: 0.3202 time to fit residues: 198.0543 Evaluate side-chains 424 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 383 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 81 optimal weight: 7.9990 chunk 150 optimal weight: 0.4980 chunk 196 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 841 ASN B 187 GLN B 194 ASN B 998 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.160626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.122259 restraints weight = 19868.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.122936 restraints weight = 15658.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.123243 restraints weight = 16431.706| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16409 Z= 0.198 Angle : 0.615 11.218 22223 Z= 0.304 Chirality : 0.043 0.254 2506 Planarity : 0.005 0.102 2908 Dihedral : 4.171 42.951 2216 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.17 % Allowed : 20.24 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 2008 helix: 2.43 (0.15), residues: 1112 sheet: -0.68 (0.49), residues: 103 loop : -0.83 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 711 HIS 0.004 0.001 HIS B1267 PHE 0.021 0.002 PHE A 742 TYR 0.016 0.002 TYR B1550 ARG 0.009 0.001 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 876) hydrogen bonds : angle 3.99352 ( 2562) SS BOND : bond 0.00423 ( 1) SS BOND : angle 1.03546 ( 2) covalent geometry : bond 0.00477 (16408) covalent geometry : angle 0.61529 (22221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 407 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8708 (t70) cc_final: 0.8323 (t0) REVERT: A 338 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 397 GLU cc_start: 0.8500 (tp30) cc_final: 0.7835 (tm-30) REVERT: A 518 ASN cc_start: 0.8507 (m-40) cc_final: 0.8060 (m110) REVERT: A 527 ASN cc_start: 0.8833 (t0) cc_final: 0.8292 (t0) REVERT: A 549 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8103 (mmpt) REVERT: A 628 SER cc_start: 0.8266 (m) cc_final: 0.8031 (p) REVERT: A 639 LYS cc_start: 0.8228 (tppt) cc_final: 0.7794 (tppt) REVERT: A 671 TYR cc_start: 0.9152 (m-80) cc_final: 0.8561 (m-80) REVERT: A 747 MET cc_start: 0.8323 (tpp) cc_final: 0.8001 (tpp) REVERT: A 834 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: A 999 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8066 (ttp80) REVERT: B 139 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8506 (mm-30) REVERT: B 509 ARG cc_start: 0.6759 (ttm-80) cc_final: 0.6338 (mtp85) REVERT: B 598 ASN cc_start: 0.8577 (m-40) cc_final: 0.8200 (m-40) REVERT: B 879 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8961 (tt) REVERT: B 881 ASP cc_start: 0.7452 (m-30) cc_final: 0.7228 (m-30) REVERT: B 1065 ARG cc_start: 0.8623 (ptp-170) cc_final: 0.8311 (mtt180) REVERT: B 1078 TYR cc_start: 0.9389 (t80) cc_final: 0.9122 (t80) REVERT: B 1104 ASP cc_start: 0.8531 (m-30) cc_final: 0.8157 (m-30) REVERT: B 1116 ASP cc_start: 0.7798 (t0) cc_final: 0.7454 (t0) REVERT: B 1121 ASP cc_start: 0.7986 (m-30) cc_final: 0.7596 (m-30) REVERT: B 1181 GLU cc_start: 0.7275 (pt0) cc_final: 0.6972 (pt0) REVERT: B 1522 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8658 (mtpt) outliers start: 56 outliers final: 46 residues processed: 441 average time/residue: 0.3107 time to fit residues: 200.1076 Evaluate side-chains 434 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1490 THR Chi-restraints excluded: chain B residue 1632 THR Chi-restraints excluded: chain B residue 1687 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS A 744 ASN A 841 ASN B 187 GLN B 194 ASN B 969 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.182676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.142902 restraints weight = 19910.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.141260 restraints weight = 13041.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.142267 restraints weight = 14612.473| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16409 Z= 0.140 Angle : 0.582 11.385 22223 Z= 0.288 Chirality : 0.041 0.242 2506 Planarity : 0.005 0.078 2908 Dihedral : 4.128 40.239 2216 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.66 % Allowed : 20.75 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 2008 helix: 2.50 (0.15), residues: 1111 sheet: -0.67 (0.48), residues: 103 loop : -0.78 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 711 HIS 0.005 0.001 HIS A 717 PHE 0.024 0.001 PHE A 742 TYR 0.030 0.001 TYR A 546 ARG 0.008 0.000 ARG B1626 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 876) hydrogen bonds : angle 3.89830 ( 2562) SS BOND : bond 0.00447 ( 1) SS BOND : angle 0.94787 ( 2) covalent geometry : bond 0.00327 (16408) covalent geometry : angle 0.58201 (22221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 386 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8646 (t70) cc_final: 0.8277 (t0) REVERT: A 328 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 518 ASN cc_start: 0.8542 (m-40) cc_final: 0.8117 (m110) REVERT: A 527 ASN cc_start: 0.8799 (t0) cc_final: 0.8231 (t0) REVERT: A 549 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8092 (mmpt) REVERT: A 628 SER cc_start: 0.8201 (m) cc_final: 0.7960 (p) REVERT: A 639 LYS cc_start: 0.8204 (tppt) cc_final: 0.7773 (tppt) REVERT: A 747 MET cc_start: 0.8303 (tpp) cc_final: 0.7982 (tpp) REVERT: A 834 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 999 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8093 (ttp80) REVERT: B 139 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8459 (mm-30) REVERT: B 509 ARG cc_start: 0.6683 (ttm-80) cc_final: 0.6281 (mtp85) REVERT: B 598 ASN cc_start: 0.8579 (m-40) cc_final: 0.8188 (m-40) REVERT: B 879 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8910 (tt) REVERT: B 881 ASP cc_start: 0.7398 (m-30) cc_final: 0.7183 (m-30) REVERT: B 1065 ARG cc_start: 0.8595 (ptp-170) cc_final: 0.8273 (mtt180) REVERT: B 1078 TYR cc_start: 0.9362 (t80) cc_final: 0.9105 (t80) REVERT: B 1104 ASP cc_start: 0.8479 (m-30) cc_final: 0.8102 (m-30) REVERT: B 1116 ASP cc_start: 0.7727 (t0) cc_final: 0.7326 (t0) REVERT: B 1121 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: B 1181 GLU cc_start: 0.7278 (pt0) cc_final: 0.6982 (pt0) REVERT: B 1253 ASP cc_start: 0.8644 (t0) cc_final: 0.7840 (m-30) REVERT: B 1658 ASP cc_start: 0.8181 (t0) cc_final: 0.7897 (t0) outliers start: 47 outliers final: 41 residues processed: 416 average time/residue: 0.3380 time to fit residues: 205.8678 Evaluate side-chains 425 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 920 MET Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 981 ASP Chi-restraints excluded: chain B residue 1018 ASN Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1121 ASP Chi-restraints excluded: chain B residue 1154 GLU Chi-restraints excluded: chain B residue 1179 LEU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain B residue 1256 SER Chi-restraints excluded: chain B residue 1271 SER Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS A 744 ASN A 841 ASN B 969 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.182669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.142942 restraints weight = 19760.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.141440 restraints weight = 12859.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.142254 restraints weight = 14773.471| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 16409 Z= 0.171 Angle : 0.806 59.200 22223 Z= 0.453 Chirality : 0.041 0.234 2506 Planarity : 0.005 0.081 2908 Dihedral : 4.130 40.218 2216 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.66 % Allowed : 20.98 % Favored : 76.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.19), residues: 2008 helix: 2.50 (0.15), residues: 1111 sheet: -0.67 (0.48), residues: 103 loop : -0.77 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 711 HIS 0.004 0.001 HIS A 717 PHE 0.022 0.001 PHE A 742 TYR 0.025 0.001 TYR A 546 ARG 0.007 0.000 ARG A 740 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 876) hydrogen bonds : angle 3.89730 ( 2562) SS BOND : bond 0.00439 ( 1) SS BOND : angle 0.95208 ( 2) covalent geometry : bond 0.00359 (16408) covalent geometry : angle 0.80606 (22221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6203.32 seconds wall clock time: 108 minutes 26.73 seconds (6506.73 seconds total)