Starting phenix.real_space_refine on Sat Nov 16 14:47:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sql_40709/11_2024/8sql_40709.cif" } resolution = 3.1 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= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 C 7271 2.51 5 N 1871 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11218 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 11078 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 42, 'TRANS': 1353} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Time building chain proxies: 6.85, per 1000 atoms: 0.61 Number of scatterers: 11218 At special positions: 0 Unit cell: (85.49, 108.15, 153.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 2 15.00 O 2023 8.00 N 1871 7.00 C 7271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 73.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 36 through 60 removed outlier: 4.185A pdb=" N LYS A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 94 removed outlier: 3.649A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.656A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 165 through 189 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.151A pdb=" N SER A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.796A pdb=" N ASN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 323 removed outlier: 6.023A pdb=" N SER A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 341 through 392 removed outlier: 3.947A pdb=" N GLY A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 411 through 424 removed outlier: 3.533A pdb=" N LEU A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 447 through 493 removed outlier: 4.097A pdb=" N GLY A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 517 through 555 removed outlier: 3.518A pdb=" N LYS A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 4.029A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 603 removed outlier: 3.909A pdb=" N PHE A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Proline residue: A 566 - end of helix removed outlier: 3.989A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.730A pdb=" N LEU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 730 through 738 removed outlier: 4.472A pdb=" N ASP A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.691A pdb=" N ILE A 751 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.757A pdb=" N ARG A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 783 removed outlier: 3.760A pdb=" N ALA A 781 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 813 through 820 removed outlier: 3.578A pdb=" N LEU A 817 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.513A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 982 Processing helix chain 'A' and resid 987 through 1016 Processing helix chain 'A' and resid 1017 through 1035 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.738A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1055 removed outlier: 3.643A pdb=" N ARG A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE A1053 " --> pdb=" O ILE A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 Processing helix chain 'A' and resid 1063 through 1089 Processing helix chain 'A' and resid 1092 through 1138 Proline residue: A1098 - end of helix removed outlier: 3.732A pdb=" N ARG A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1138 through 1145 Processing helix chain 'A' and resid 1147 through 1201 Proline residue: A1168 - end of helix removed outlier: 3.742A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1248 removed outlier: 3.548A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A1224 " --> pdb=" O THR A1220 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1320 removed outlier: 4.375A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1340 No H-bonds generated for 'chain 'A' and resid 1338 through 1340' Processing helix chain 'A' and resid 1341 through 1347 Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1374 through 1385 Processing helix chain 'A' and resid 1387 through 1395 Processing helix chain 'A' and resid 1397 through 1400 Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.679A pdb=" N VAL A1426 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1456 Processing helix chain 'A' and resid 1467 through 1471 Processing helix chain 'A' and resid 1490 through 1498 removed outlier: 4.044A pdb=" N ASN A1498 " --> pdb=" O LEU A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1506 Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.609A pdb=" N VAL A 689 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 688 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 626 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 628 " --> pdb=" O PHE A 651 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE A 651 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 630 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 649 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 632 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A 647 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.609A pdb=" N VAL A 689 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 688 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 626 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 633 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 681 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.392A pdb=" N ASP A 827 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AA5, first strand: chain 'A' and resid 1289 through 1292 removed outlier: 5.479A pdb=" N LYS A1290 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A1279 " --> pdb=" O LYS A1290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1289 through 1292 removed outlier: 5.479A pdb=" N LYS A1290 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR A1279 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A1272 " --> pdb=" O ILE A1332 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A1332 " --> pdb=" O ILE A1272 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE A1274 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A1330 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A1276 " --> pdb=" O GLY A1328 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A1328 " --> pdb=" O ASN A1276 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER A1278 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1350 through 1352 removed outlier: 6.476A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A1302 " --> pdb=" O THR A1463 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS A1301 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU A1480 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A1305 " --> pdb=" O LEU A1480 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1362 760 hydrogen bonds defined for protein. 2238 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: 4.12 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1776 1.31 - 1.43: 3026 1.43 - 1.56: 6552 1.56 - 1.68: 5 1.68 - 1.81: 83 Bond restraints: 11442 Sorted by residual: bond pdb=" C8 PTY A1602 " pdb=" O7 PTY A1602 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C8 PTY A1601 " pdb=" O7 PTY A1601 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C30 PTY A1601 " pdb=" O4 PTY A1601 " ideal model delta sigma weight residual 1.331 1.395 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C30 PTY A1602 " pdb=" O4 PTY A1602 " ideal model delta sigma weight residual 1.331 1.392 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" CA VAL A1485 " pdb=" CB VAL A1485 " ideal model delta sigma weight residual 1.538 1.564 -0.025 1.06e-02 8.90e+03 5.79e+00 ... (remaining 11437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 15415 3.47 - 6.94: 66 6.94 - 10.41: 9 10.41 - 13.88: 3 13.88 - 17.35: 2 Bond angle restraints: 15495 Sorted by residual: angle pdb=" N LEU A 646 " pdb=" CA LEU A 646 " pdb=" C LEU A 646 " ideal model delta sigma weight residual 109.59 97.52 12.07 1.47e+00 4.63e-01 6.74e+01 angle pdb=" N LYS A 647 " pdb=" CA LYS A 647 " pdb=" C LYS A 647 " ideal model delta sigma weight residual 109.14 120.49 -11.35 1.49e+00 4.50e-01 5.80e+01 angle pdb=" N LYS A1484 " pdb=" CA LYS A1484 " pdb=" C LYS A1484 " ideal model delta sigma weight residual 108.96 99.39 9.57 1.59e+00 3.96e-01 3.62e+01 angle pdb=" O11 PTY A1601 " pdb=" P1 PTY A1601 " pdb=" O14 PTY A1601 " ideal model delta sigma weight residual 92.90 110.25 -17.35 3.00e+00 1.11e-01 3.34e+01 angle pdb=" O11 PTY A1602 " pdb=" P1 PTY A1602 " pdb=" O14 PTY A1602 " ideal model delta sigma weight residual 92.90 109.70 -16.80 3.00e+00 1.11e-01 3.14e+01 ... (remaining 15490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 6723 33.90 - 67.80: 115 67.80 - 101.71: 16 101.71 - 135.61: 0 135.61 - 169.51: 1 Dihedral angle restraints: 6855 sinusoidal: 2730 harmonic: 4125 Sorted by residual: dihedral pdb=" CA LYS A 58 " pdb=" C LYS A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta harmonic sigma weight residual -180.00 -151.45 -28.55 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LEU A1387 " pdb=" C LEU A1387 " pdb=" N LYS A1388 " pdb=" CA LYS A1388 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A1489 " pdb=" C ASP A1489 " pdb=" N SER A1490 " pdb=" CA SER A1490 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 6852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1370 0.044 - 0.089: 353 0.089 - 0.133: 77 0.133 - 0.177: 3 0.177 - 0.221: 2 Chirality restraints: 1805 Sorted by residual: chirality pdb=" CA LYS A1484 " pdb=" N LYS A1484 " pdb=" C LYS A1484 " pdb=" CB LYS A1484 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 646 " pdb=" N LEU A 646 " pdb=" C LEU A 646 " pdb=" CB LEU A 646 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL A1485 " pdb=" N VAL A1485 " pdb=" C VAL A1485 " pdb=" CB VAL A1485 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 1802 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A1282 " -0.059 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A1283 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A1283 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A1283 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 46 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ILE A 46 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 46 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 47 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 514 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C ARG A 514 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 514 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 515 " -0.012 2.00e-02 2.50e+03 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 19 2.40 - 3.03: 7411 3.03 - 3.65: 17639 3.65 - 4.28: 26741 4.28 - 4.90: 44804 Nonbonded interactions: 96614 Sorted by model distance: nonbonded pdb=" OG1 THR A 836 " pdb=" OE1 GLU A 839 " model vdw 1.781 3.040 nonbonded pdb=" OG SER A1022 " pdb=" OD1 ASP A1061 " model vdw 1.904 3.040 nonbonded pdb=" OD1 ASN A 69 " pdb=" N TRP A 70 " model vdw 2.136 3.120 nonbonded pdb=" O PRO A1298 " pdb=" OG1 THR A1460 " model vdw 2.163 3.040 nonbonded pdb=" OG SER A1114 " pdb=" NH1 ARG A1118 " model vdw 2.195 3.120 ... (remaining 96609 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11442 Z= 0.290 Angle : 0.752 17.350 15495 Z= 0.410 Chirality : 0.041 0.221 1805 Planarity : 0.004 0.088 1924 Dihedral : 14.012 169.509 4185 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.16 % Allowed : 0.25 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1386 helix: 0.54 (0.16), residues: 932 sheet: 0.25 (0.63), residues: 56 loop : -0.54 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 70 HIS 0.006 0.001 HIS A 364 PHE 0.018 0.002 PHE A 954 TYR 0.016 0.002 TYR A1105 ARG 0.010 0.001 ARG A1035 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8538 (mm) cc_final: 0.8253 (mt) REVERT: A 195 MET cc_start: 0.5187 (ttm) cc_final: 0.4878 (tpp) REVERT: A 268 LYS cc_start: 0.8290 (pptt) cc_final: 0.8045 (pttt) REVERT: A 529 MET cc_start: 0.7468 (ttt) cc_final: 0.7158 (ttt) REVERT: A 777 ASP cc_start: 0.7532 (t0) cc_final: 0.7245 (t70) REVERT: A 1390 HIS cc_start: 0.5926 (t70) cc_final: 0.5667 (t70) outliers start: 2 outliers final: 2 residues processed: 215 average time/residue: 0.2273 time to fit residues: 71.4812 Evaluate side-chains 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 127 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 637 GLN A 698 GLN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 GLN A1414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11442 Z= 0.258 Angle : 0.659 9.155 15495 Z= 0.344 Chirality : 0.044 0.171 1805 Planarity : 0.005 0.056 1924 Dihedral : 9.093 161.936 1581 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.91 % Allowed : 6.17 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1386 helix: 1.01 (0.16), residues: 936 sheet: 0.78 (0.68), residues: 56 loop : -0.24 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.003 0.001 HIS A1026 PHE 0.019 0.002 PHE A 464 TYR 0.021 0.002 TYR A 695 ARG 0.005 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 43 ILE cc_start: 0.8505 (mm) cc_final: 0.8209 (mt) REVERT: A 154 LEU cc_start: 0.8618 (tp) cc_final: 0.8317 (mt) REVERT: A 268 LYS cc_start: 0.8340 (pptt) cc_final: 0.8038 (pttt) outliers start: 11 outliers final: 8 residues processed: 173 average time/residue: 0.2238 time to fit residues: 58.0624 Evaluate side-chains 150 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN A 535 GLN A1147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11442 Z= 0.278 Angle : 0.620 9.221 15495 Z= 0.322 Chirality : 0.043 0.186 1805 Planarity : 0.004 0.052 1924 Dihedral : 8.457 144.369 1579 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 7.65 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1386 helix: 1.10 (0.16), residues: 939 sheet: 0.82 (0.69), residues: 55 loop : -0.27 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.004 0.001 HIS A 364 PHE 0.019 0.002 PHE A 464 TYR 0.018 0.002 TYR A 722 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.185 Fit side-chains REVERT: A 43 ILE cc_start: 0.8545 (mm) cc_final: 0.8229 (mt) REVERT: A 154 LEU cc_start: 0.8612 (tp) cc_final: 0.8297 (mt) REVERT: A 268 LYS cc_start: 0.8407 (pptt) cc_final: 0.7999 (pttt) REVERT: A 309 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7305 (ttp80) REVERT: A 962 MET cc_start: 0.7805 (tpp) cc_final: 0.7561 (tpp) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.2213 time to fit residues: 55.1548 Evaluate side-chains 158 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A 535 GLN A 637 GLN A 657 ASN A1055 ASN A1390 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11442 Z= 0.280 Angle : 0.602 9.048 15495 Z= 0.313 Chirality : 0.042 0.188 1805 Planarity : 0.004 0.055 1924 Dihedral : 8.014 127.994 1579 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.98 % Allowed : 9.38 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1386 helix: 1.13 (0.16), residues: 941 sheet: 0.56 (0.65), residues: 60 loop : -0.23 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.008 0.001 HIS A1390 PHE 0.022 0.002 PHE A 713 TYR 0.017 0.001 TYR A1105 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.254 Fit side-chains REVERT: A 154 LEU cc_start: 0.8609 (tp) cc_final: 0.8311 (mt) REVERT: A 268 LYS cc_start: 0.8343 (pptt) cc_final: 0.7998 (pttt) REVERT: A 269 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 309 ARG cc_start: 0.7533 (ttt180) cc_final: 0.7288 (ttp80) outliers start: 24 outliers final: 16 residues processed: 165 average time/residue: 0.2129 time to fit residues: 53.6811 Evaluate side-chains 154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 GLN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1147 GLN A1390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11442 Z= 0.216 Angle : 0.576 8.888 15495 Z= 0.299 Chirality : 0.041 0.191 1805 Planarity : 0.004 0.054 1924 Dihedral : 7.540 105.503 1579 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.89 % Allowed : 11.11 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1386 helix: 1.31 (0.16), residues: 938 sheet: 0.62 (0.68), residues: 59 loop : -0.25 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 70 HIS 0.006 0.001 HIS A1390 PHE 0.019 0.001 PHE A 464 TYR 0.016 0.001 TYR A1105 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.7902 (mt) cc_final: 0.7598 (mp) REVERT: A 154 LEU cc_start: 0.8545 (tp) cc_final: 0.8277 (mt) REVERT: A 309 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7290 (ttp80) REVERT: A 462 ASN cc_start: 0.7951 (t0) cc_final: 0.7709 (t0) REVERT: A 777 ASP cc_start: 0.7610 (t0) cc_final: 0.7244 (t70) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 0.2278 time to fit residues: 56.5207 Evaluate side-chains 153 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A1390 HIS A1449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11442 Z= 0.321 Angle : 0.616 9.074 15495 Z= 0.318 Chirality : 0.043 0.201 1805 Planarity : 0.004 0.057 1924 Dihedral : 7.293 88.787 1579 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 12.35 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1386 helix: 1.25 (0.16), residues: 934 sheet: 0.57 (0.68), residues: 59 loop : -0.26 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 70 HIS 0.008 0.001 HIS A1390 PHE 0.020 0.002 PHE A 464 TYR 0.019 0.002 TYR A1105 ARG 0.004 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8609 (tp) cc_final: 0.8313 (mt) REVERT: A 309 ARG cc_start: 0.7556 (ttt180) cc_final: 0.7303 (ttp80) REVERT: A 777 ASP cc_start: 0.7499 (t0) cc_final: 0.7231 (t0) outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 0.2248 time to fit residues: 52.7560 Evaluate side-chains 143 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.0030 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1147 GLN A1390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11442 Z= 0.234 Angle : 0.591 12.012 15495 Z= 0.303 Chirality : 0.041 0.201 1805 Planarity : 0.004 0.055 1924 Dihedral : 6.909 84.977 1579 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.81 % Allowed : 13.09 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1386 helix: 1.35 (0.16), residues: 937 sheet: 0.89 (0.71), residues: 54 loop : -0.32 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1175 HIS 0.008 0.001 HIS A1390 PHE 0.022 0.001 PHE A 464 TYR 0.016 0.001 TYR A1105 ARG 0.003 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8536 (tp) cc_final: 0.8282 (mt) REVERT: A 309 ARG cc_start: 0.7576 (ttt180) cc_final: 0.7322 (ttp80) REVERT: A 777 ASP cc_start: 0.7633 (t0) cc_final: 0.7281 (t70) REVERT: A 1176 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7975 (tp) outliers start: 22 outliers final: 17 residues processed: 157 average time/residue: 0.2385 time to fit residues: 57.6517 Evaluate side-chains 146 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.4980 chunk 80 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A1390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11442 Z= 0.213 Angle : 0.594 12.213 15495 Z= 0.306 Chirality : 0.041 0.205 1805 Planarity : 0.004 0.055 1924 Dihedral : 6.682 83.184 1579 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.06 % Allowed : 14.16 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1386 helix: 1.41 (0.16), residues: 938 sheet: 0.78 (0.71), residues: 54 loop : -0.35 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1175 HIS 0.005 0.001 HIS A1390 PHE 0.025 0.001 PHE A 464 TYR 0.016 0.001 TYR A1105 ARG 0.003 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8377 (mmm) cc_final: 0.8102 (mmm) REVERT: A 154 LEU cc_start: 0.8522 (tp) cc_final: 0.8294 (mt) REVERT: A 309 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7309 (ttp80) REVERT: A 777 ASP cc_start: 0.7624 (t0) cc_final: 0.7302 (t70) REVERT: A 1176 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8047 (tp) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.2234 time to fit residues: 51.4920 Evaluate side-chains 149 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1386 HIS Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A1147 GLN A1390 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11442 Z= 0.227 Angle : 0.596 11.406 15495 Z= 0.305 Chirality : 0.041 0.199 1805 Planarity : 0.004 0.055 1924 Dihedral : 6.468 80.438 1579 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.98 % Allowed : 14.90 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1386 helix: 1.43 (0.16), residues: 939 sheet: 0.80 (0.72), residues: 54 loop : -0.40 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 636 HIS 0.004 0.001 HIS A 364 PHE 0.027 0.001 PHE A 464 TYR 0.017 0.001 TYR A1105 ARG 0.003 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.8369 (mmm) cc_final: 0.8135 (mmm) REVERT: A 154 LEU cc_start: 0.8539 (tp) cc_final: 0.8320 (mt) REVERT: A 309 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7313 (ttp80) REVERT: A 777 ASP cc_start: 0.7644 (t0) cc_final: 0.7364 (t0) REVERT: A 1176 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8070 (tp) outliers start: 24 outliers final: 21 residues processed: 156 average time/residue: 0.2087 time to fit residues: 49.5730 Evaluate side-chains 154 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1386 HIS Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A1147 GLN A1390 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11442 Z= 0.209 Angle : 0.588 9.984 15495 Z= 0.303 Chirality : 0.041 0.205 1805 Planarity : 0.004 0.055 1924 Dihedral : 6.333 78.741 1579 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 15.23 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1386 helix: 1.46 (0.17), residues: 943 sheet: 0.72 (0.71), residues: 54 loop : -0.41 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.008 0.001 HIS A1390 PHE 0.032 0.001 PHE A 464 TYR 0.016 0.001 TYR A1105 ARG 0.003 0.000 ARG A 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8503 (tp) cc_final: 0.8301 (mt) REVERT: A 309 ARG cc_start: 0.7546 (ttt180) cc_final: 0.7310 (ttp80) REVERT: A 777 ASP cc_start: 0.7718 (t0) cc_final: 0.7430 (t0) REVERT: A 1176 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 1416 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7627 (tp-100) outliers start: 20 outliers final: 19 residues processed: 153 average time/residue: 0.2177 time to fit residues: 50.3102 Evaluate side-chains 152 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 980 SER Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1147 GLN Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN A1147 GLN A1390 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.175974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117803 restraints weight = 12455.518| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.27 r_work: 0.3253 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11442 Z= 0.239 Angle : 0.596 10.233 15495 Z= 0.305 Chirality : 0.042 0.214 1805 Planarity : 0.004 0.055 1924 Dihedral : 6.255 76.821 1579 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.98 % Allowed : 14.98 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1386 helix: 1.46 (0.16), residues: 941 sheet: 0.65 (0.70), residues: 54 loop : -0.41 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.008 0.001 HIS A1390 PHE 0.031 0.001 PHE A 464 TYR 0.016 0.001 TYR A1105 ARG 0.003 0.000 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.80 seconds wall clock time: 49 minutes 13.63 seconds (2953.63 seconds total)