Starting phenix.real_space_refine on Tue Dec 31 01:03:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.map" model { file = "/net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcc_9067/12_2024/6mcc_9067.cif" } resolution = 3.9 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= 0.005 sd= 0.088 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 118 5.49 5 S 26 5.16 5 C 8551 2.51 5 N 2458 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14175 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10715 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 507 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 966 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLU:plan': 17, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 8.26, per 1000 atoms: 0.58 Number of scatterers: 14175 At special positions: 0 Unit cell: (92, 121.9, 144.9, 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 26 16.00 P 118 15.00 O 3022 8.00 N 2458 7.00 C 8551 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 46.4% alpha, 8.6% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 60 through 86 removed outlier: 3.587A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.636A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 144 removed outlier: 4.407A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.583A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.901A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.212A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 5.250A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.806A pdb=" N ASN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 317 through 340 removed outlier: 3.503A pdb=" N MET A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.689A pdb=" N ILE A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.545A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 411 through 425 removed outlier: 4.337A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.771A pdb=" N ASP A 435 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 474 through 478 removed outlier: 4.130A pdb=" N PHE A 478 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.670A pdb=" N GLU A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.802A pdb=" N ASP A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.648A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 4.187A pdb=" N GLU A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 635' Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.767A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 702 through 712 removed outlier: 4.540A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.280A pdb=" N LYS A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.868A pdb=" N LYS A 772 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 773 " --> pdb=" O THR A 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 769 through 773' Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.954A pdb=" N GLU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 791 removed outlier: 3.934A pdb=" N GLU A 785 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 808 through 816 Processing helix chain 'A' and resid 860 through 864 Processing helix chain 'A' and resid 872 through 879 removed outlier: 3.537A pdb=" N MET A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 889 removed outlier: 3.727A pdb=" N ARG A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 885 " --> pdb=" O ASN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.796A pdb=" N PHE A 897 " --> pdb=" O THR A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 removed outlier: 3.862A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.613A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.306A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.591A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 986 " --> pdb=" O HIS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 removed outlier: 3.941A pdb=" N GLU A1005 " --> pdb=" O PRO A1002 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A1006 " --> pdb=" O LYS A1003 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1006' Processing helix chain 'A' and resid 1041 through 1046 removed outlier: 3.509A pdb=" N ASN A1044 " --> pdb=" O ASN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1078 Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.188A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.637A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1266 removed outlier: 3.733A pdb=" N LEU A1266 " --> pdb=" O LYS A1263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1268 through 1281 Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.695A pdb=" N LEU A1287 " --> pdb=" O ALA A1283 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 3.969A pdb=" N GLU A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.530A pdb=" N LEU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.592A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 5.952A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1215 " --> pdb=" O GLU A1219 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.408A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.515A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA7, first strand: chain 'A' and resid 1064 through 1065 removed outlier: 7.548A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1073 " --> pdb=" O GLU A1064 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.674A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 72 removed outlier: 5.830A pdb=" N CYS C 70 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN C 90 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP C 72 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 78 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 72 removed outlier: 5.830A pdb=" N CYS C 70 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN C 90 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP C 72 " --> pdb=" O PHE C 88 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 39 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 127 " --> pdb=" O ILE C 40 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 8.11 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2348 1.32 - 1.44: 4340 1.44 - 1.57: 7714 1.57 - 1.69: 232 1.69 - 1.81: 48 Bond restraints: 14682 Sorted by residual: bond pdb=" C6 GTP B 1 " pdb=" O6 GTP B 1 " ideal model delta sigma weight residual 1.230 1.387 -0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.458 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O3B GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sigma weight residual 1.610 1.550 0.060 2.00e-02 2.50e+03 9.00e+00 bond pdb=" C2 GTP B 1 " pdb=" N1 GTP B 1 " ideal model delta sigma weight residual 1.380 1.438 -0.058 2.00e-02 2.50e+03 8.37e+00 ... (remaining 14677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 19768 2.54 - 5.08: 564 5.08 - 7.62: 78 7.62 - 10.16: 18 10.16 - 12.69: 7 Bond angle restraints: 20435 Sorted by residual: angle pdb=" C ASP A 353 " pdb=" N GLN A 354 " pdb=" CA GLN A 354 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ASP C 101 " pdb=" N GLU C 102 " pdb=" CA GLU C 102 " ideal model delta sigma weight residual 121.54 131.54 -10.00 1.91e+00 2.74e-01 2.74e+01 angle pdb=" CA THR C 107 " pdb=" CB THR C 107 " pdb=" CG2 THR C 107 " ideal model delta sigma weight residual 110.50 118.04 -7.54 1.70e+00 3.46e-01 1.97e+01 angle pdb=" N GLY A1133 " pdb=" CA GLY A1133 " pdb=" C GLY A1133 " ideal model delta sigma weight residual 110.20 115.93 -5.73 1.32e+00 5.74e-01 1.89e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.65 -6.45 1.50e+00 4.44e-01 1.85e+01 ... (remaining 20430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8552 35.47 - 70.95: 366 70.95 - 106.42: 39 106.42 - 141.90: 1 141.90 - 177.37: 4 Dihedral angle restraints: 8962 sinusoidal: 4561 harmonic: 4401 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 40.60 159.40 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.24 175.76 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA THR C 107 " pdb=" C THR C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta harmonic sigma weight residual -180.00 -145.35 -34.65 0 5.00e+00 4.00e-02 4.80e+01 ... (remaining 8959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.963: 2409 0.963 - 1.925: 0 1.925 - 2.888: 0 2.888 - 3.851: 0 3.851 - 4.814: 2 Chirality restraints: 2411 Sorted by residual: chirality pdb=" C2' GTP B 1 " pdb=" C1' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" O2' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.34 -4.81 2.00e-01 2.50e+01 5.79e+02 chirality pdb=" C4' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O4' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 2.25 -4.72 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" C1' A B 8 " pdb=" O4' A B 8 " pdb=" C2' A B 8 " pdb=" N9 A B 8 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2408 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 8 " -0.035 2.00e-02 2.50e+03 1.80e-02 8.94e+00 pdb=" N9 A B 8 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 8 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 8 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 8 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 8 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 8 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 8 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C LEU A 302 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 302 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 303 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 295 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C ASN A 295 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 295 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4102 2.81 - 3.33: 12894 3.33 - 3.86: 24534 3.86 - 4.38: 26463 4.38 - 4.90: 42149 Nonbonded interactions: 110142 Sorted by model distance: nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.290 3.040 nonbonded pdb=" O2' U B 62 " pdb=" OE1 GLN A 402 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.317 3.040 nonbonded pdb=" O TYR A 136 " pdb=" OG SER A 318 " model vdw 2.319 3.040 nonbonded pdb=" O ARG A 925 " pdb=" OG1 THR A 928 " model vdw 2.328 3.040 ... (remaining 110137 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: 0.420 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.157 14682 Z= 0.400 Angle : 1.038 12.694 20435 Z= 0.537 Chirality : 0.148 4.814 2411 Planarity : 0.006 0.052 2194 Dihedral : 17.836 177.369 6114 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.08 % Allowed : 9.35 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.52 (0.17), residues: 1490 helix: -3.23 (0.14), residues: 609 sheet: -1.76 (0.45), residues: 111 loop : -3.02 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 476 HIS 0.009 0.002 HIS A 160 PHE 0.044 0.003 PHE A1008 TYR 0.023 0.003 TYR A 72 ARG 0.022 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8879 (p-90) cc_final: 0.8612 (p-90) REVERT: A 241 LEU cc_start: 0.9103 (mm) cc_final: 0.8611 (pp) REVERT: A 586 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8452 (mtm-85) REVERT: A 879 MET cc_start: 0.7602 (mtt) cc_final: 0.7231 (mtt) REVERT: A 883 TRP cc_start: 0.6278 (m-10) cc_final: 0.5804 (m-10) REVERT: A 1205 GLU cc_start: 0.8032 (tt0) cc_final: 0.7777 (tt0) REVERT: C 75 PHE cc_start: 0.8124 (p90) cc_final: 0.7699 (p90) outliers start: 13 outliers final: 3 residues processed: 249 average time/residue: 0.2777 time to fit residues: 100.2310 Evaluate side-chains 147 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 662 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 522 ASN A 831 ASN A 930 HIS A 980 ASN A 985 HIS A 990 ASN A1054 ASN A1093 ASN A1101 GLN A1297 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14682 Z= 0.177 Angle : 0.679 13.403 20435 Z= 0.337 Chirality : 0.040 0.206 2411 Planarity : 0.004 0.047 2194 Dihedral : 19.688 175.287 3378 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.14 % Allowed : 13.65 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -3.27 (0.19), residues: 1490 helix: -1.75 (0.18), residues: 628 sheet: -1.37 (0.45), residues: 115 loop : -2.69 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.032 0.002 PHE A1008 TYR 0.014 0.001 TYR A 812 ARG 0.005 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8756 (p-90) cc_final: 0.8215 (p-90) REVERT: A 684 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7880 (tttt) REVERT: A 706 GLU cc_start: 0.7883 (mp0) cc_final: 0.7443 (mp0) REVERT: A 879 MET cc_start: 0.7870 (mtt) cc_final: 0.7379 (mtt) REVERT: A 1046 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: A 1074 TRP cc_start: 0.4880 (t60) cc_final: 0.4665 (t60) REVERT: A 1205 GLU cc_start: 0.8071 (tt0) cc_final: 0.7725 (tt0) REVERT: A 1365 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8411 (tt) REVERT: C 25 ARG cc_start: 0.7792 (tmm-80) cc_final: 0.7528 (tmm-80) REVERT: C 120 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8781 (tp) outliers start: 38 outliers final: 13 residues processed: 211 average time/residue: 0.2507 time to fit residues: 80.7750 Evaluate side-chains 161 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 116 optimal weight: 30.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 369 GLN A 489 GLN A 739 GLN A 817 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14682 Z= 0.363 Angle : 0.751 11.582 20435 Z= 0.380 Chirality : 0.044 0.202 2411 Planarity : 0.004 0.047 2194 Dihedral : 19.667 178.306 3378 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.21 % Allowed : 15.47 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1490 helix: -1.11 (0.19), residues: 624 sheet: -1.39 (0.46), residues: 113 loop : -2.41 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 476 HIS 0.009 0.002 HIS A 412 PHE 0.032 0.002 PHE A1008 TYR 0.023 0.002 TYR A 136 ARG 0.006 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8893 (p-90) cc_final: 0.8238 (p-90) REVERT: A 76 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8709 (ttpt) REVERT: A 84 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 152 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8670 (ptt90) REVERT: A 241 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8606 (pp) REVERT: A 684 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (tttt) REVERT: A 706 GLU cc_start: 0.7878 (mp0) cc_final: 0.7454 (mp0) REVERT: A 759 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 786 GLU cc_start: 0.8828 (tt0) cc_final: 0.8313 (tp30) REVERT: A 879 MET cc_start: 0.7732 (mtt) cc_final: 0.7318 (mtt) REVERT: A 920 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7999 (tm-30) REVERT: A 1021 MET cc_start: 0.7979 (tpp) cc_final: 0.7645 (tpp) REVERT: A 1046 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: A 1118 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8078 (tttt) REVERT: A 1164 LEU cc_start: 0.8878 (tp) cc_final: 0.8619 (tt) REVERT: A 1205 GLU cc_start: 0.8265 (tt0) cc_final: 0.7948 (tt0) REVERT: A 1313 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7078 (m-10) REVERT: A 1365 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8659 (tm) REVERT: C 97 ASP cc_start: 0.8115 (t0) cc_final: 0.7330 (p0) REVERT: C 120 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8855 (tp) outliers start: 63 outliers final: 28 residues processed: 199 average time/residue: 0.2780 time to fit residues: 85.5839 Evaluate side-chains 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 0.0570 chunk 97 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14682 Z= 0.142 Angle : 0.628 11.104 20435 Z= 0.303 Chirality : 0.039 0.175 2411 Planarity : 0.003 0.043 2194 Dihedral : 19.429 175.111 3378 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.64 % Allowed : 17.37 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1490 helix: -0.45 (0.21), residues: 625 sheet: -1.12 (0.46), residues: 117 loop : -2.18 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1074 HIS 0.004 0.001 HIS A 328 PHE 0.029 0.001 PHE A1008 TYR 0.022 0.001 TYR A 988 ARG 0.005 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8762 (p-90) cc_final: 0.8409 (p-90) REVERT: A 241 LEU cc_start: 0.9071 (mm) cc_final: 0.8625 (pp) REVERT: A 422 ILE cc_start: 0.9507 (tp) cc_final: 0.9178 (tp) REVERT: A 464 TRP cc_start: 0.8468 (p90) cc_final: 0.8223 (p90) REVERT: A 684 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7908 (tttt) REVERT: A 706 GLU cc_start: 0.7846 (mp0) cc_final: 0.7357 (mp0) REVERT: A 759 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8794 (pp) REVERT: A 786 GLU cc_start: 0.8799 (tt0) cc_final: 0.8447 (tp30) REVERT: A 879 MET cc_start: 0.7999 (mtt) cc_final: 0.7699 (mtt) REVERT: A 920 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 1021 MET cc_start: 0.7692 (tpp) cc_final: 0.7206 (tpp) REVERT: A 1089 MET cc_start: 0.8860 (mtm) cc_final: 0.8337 (ttm) REVERT: A 1205 GLU cc_start: 0.8044 (tt0) cc_final: 0.7781 (tt0) REVERT: C 97 ASP cc_start: 0.8073 (t0) cc_final: 0.7266 (p0) REVERT: C 120 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8848 (tp) outliers start: 44 outliers final: 20 residues processed: 209 average time/residue: 0.2512 time to fit residues: 80.5739 Evaluate side-chains 172 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1241 HIS A1297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14682 Z= 0.146 Angle : 0.619 14.833 20435 Z= 0.299 Chirality : 0.038 0.202 2411 Planarity : 0.003 0.042 2194 Dihedral : 19.282 176.301 3378 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.89 % Allowed : 18.69 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.68 (0.21), residues: 1490 helix: -0.15 (0.21), residues: 627 sheet: -1.00 (0.46), residues: 113 loop : -2.02 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1074 HIS 0.012 0.001 HIS A1297 PHE 0.026 0.001 PHE A1008 TYR 0.022 0.001 TYR A 988 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8795 (p-90) cc_final: 0.8344 (p-90) REVERT: A 169 LEU cc_start: 0.8754 (mt) cc_final: 0.8543 (mp) REVERT: A 241 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8658 (pp) REVERT: A 428 ASP cc_start: 0.7801 (p0) cc_final: 0.7591 (p0) REVERT: A 738 LEU cc_start: 0.8258 (tt) cc_final: 0.7852 (mm) REVERT: A 759 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8773 (pp) REVERT: A 762 GLU cc_start: 0.6681 (pm20) cc_final: 0.6458 (pm20) REVERT: A 786 GLU cc_start: 0.8769 (tt0) cc_final: 0.8560 (tp30) REVERT: A 879 MET cc_start: 0.8239 (mtt) cc_final: 0.7884 (mtt) REVERT: A 920 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 1000 LYS cc_start: 0.8397 (tmtt) cc_final: 0.8112 (tttm) REVERT: A 1021 MET cc_start: 0.7725 (tpp) cc_final: 0.7291 (tpp) REVERT: A 1089 MET cc_start: 0.8914 (mtm) cc_final: 0.8336 (ttm) REVERT: A 1164 LEU cc_start: 0.8604 (tp) cc_final: 0.8377 (tt) REVERT: C 7 LYS cc_start: 0.8500 (ptmm) cc_final: 0.8105 (ptmm) REVERT: C 120 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8865 (tp) outliers start: 47 outliers final: 23 residues processed: 208 average time/residue: 0.2350 time to fit residues: 75.6363 Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14682 Z= 0.170 Angle : 0.635 14.914 20435 Z= 0.305 Chirality : 0.039 0.189 2411 Planarity : 0.003 0.043 2194 Dihedral : 19.169 176.466 3378 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.89 % Allowed : 18.61 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.45 (0.22), residues: 1490 helix: 0.07 (0.21), residues: 629 sheet: -0.77 (0.49), residues: 109 loop : -1.94 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.025 0.001 PHE A1008 TYR 0.017 0.001 TYR A 568 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8809 (p-90) cc_final: 0.8161 (p-90) REVERT: A 241 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8708 (pp) REVERT: A 428 ASP cc_start: 0.7813 (p0) cc_final: 0.7605 (p0) REVERT: A 759 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8730 (pp) REVERT: A 879 MET cc_start: 0.8247 (mtt) cc_final: 0.7944 (mtt) REVERT: A 920 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 1000 LYS cc_start: 0.8367 (tmtt) cc_final: 0.8123 (tttm) REVERT: A 1021 MET cc_start: 0.7704 (tpp) cc_final: 0.7286 (tpp) REVERT: A 1045 PHE cc_start: 0.9123 (t80) cc_final: 0.8799 (t80) REVERT: A 1164 LEU cc_start: 0.8707 (tp) cc_final: 0.8454 (tt) REVERT: C 120 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8869 (tp) outliers start: 47 outliers final: 29 residues processed: 188 average time/residue: 0.2374 time to fit residues: 69.7180 Evaluate side-chains 176 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 695 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14682 Z= 0.281 Angle : 0.693 14.931 20435 Z= 0.344 Chirality : 0.043 0.317 2411 Planarity : 0.004 0.045 2194 Dihedral : 19.175 175.249 3378 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.97 % Allowed : 17.78 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.50 (0.22), residues: 1490 helix: 0.05 (0.21), residues: 626 sheet: -0.95 (0.49), residues: 109 loop : -1.95 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 476 HIS 0.025 0.002 HIS A 511 PHE 0.034 0.002 PHE A1008 TYR 0.017 0.002 TYR A 594 ARG 0.006 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8879 (p-90) cc_final: 0.8101 (p-90) REVERT: A 47 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7662 (tt) REVERT: A 84 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 241 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8721 (pp) REVERT: A 759 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 879 MET cc_start: 0.8020 (mtt) cc_final: 0.7559 (mtt) REVERT: A 1000 LYS cc_start: 0.8435 (tmtt) cc_final: 0.8133 (tttm) REVERT: A 1164 LEU cc_start: 0.8880 (tp) cc_final: 0.8638 (tt) REVERT: A 1313 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: C 120 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8926 (tp) outliers start: 48 outliers final: 32 residues processed: 179 average time/residue: 0.2322 time to fit residues: 65.4398 Evaluate side-chains 177 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14682 Z= 0.255 Angle : 0.686 15.134 20435 Z= 0.338 Chirality : 0.042 0.326 2411 Planarity : 0.004 0.041 2194 Dihedral : 19.118 175.292 3378 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.22 % Allowed : 18.94 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.47 (0.22), residues: 1490 helix: 0.09 (0.21), residues: 627 sheet: -1.10 (0.50), residues: 109 loop : -1.93 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A1074 HIS 0.017 0.001 HIS A 511 PHE 0.017 0.002 PHE A 916 TYR 0.037 0.002 TYR A1356 ARG 0.005 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8858 (p-90) cc_final: 0.8106 (p-90) REVERT: A 47 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 84 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 241 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8738 (pp) REVERT: A 321 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: A 712 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7965 (mm110) REVERT: A 759 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 879 MET cc_start: 0.7986 (mtt) cc_final: 0.7628 (mtt) REVERT: A 883 TRP cc_start: 0.5744 (m-10) cc_final: 0.5431 (m-90) REVERT: A 1000 LYS cc_start: 0.8412 (tmtt) cc_final: 0.8168 (tttm) REVERT: A 1045 PHE cc_start: 0.9042 (t80) cc_final: 0.8663 (t80) REVERT: A 1164 LEU cc_start: 0.8836 (tp) cc_final: 0.8575 (tt) REVERT: A 1313 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: C 7 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8274 (ptmm) REVERT: C 91 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 120 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8924 (tp) outliers start: 51 outliers final: 33 residues processed: 187 average time/residue: 0.2473 time to fit residues: 71.7832 Evaluate side-chains 184 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14682 Z= 0.184 Angle : 0.662 15.312 20435 Z= 0.320 Chirality : 0.040 0.309 2411 Planarity : 0.003 0.040 2194 Dihedral : 18.997 176.455 3378 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.47 % Allowed : 19.93 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.26 (0.22), residues: 1490 helix: 0.30 (0.21), residues: 626 sheet: -1.16 (0.48), residues: 115 loop : -1.81 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1074 HIS 0.011 0.001 HIS A 511 PHE 0.031 0.001 PHE A1008 TYR 0.026 0.001 TYR A1356 ARG 0.006 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8774 (p-90) cc_final: 0.7850 (p-90) REVERT: A 47 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7477 (tt) REVERT: A 241 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8718 (pp) REVERT: A 738 LEU cc_start: 0.8357 (tt) cc_final: 0.7721 (mt) REVERT: A 759 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 879 MET cc_start: 0.8147 (mtt) cc_final: 0.7838 (mtt) REVERT: A 883 TRP cc_start: 0.5705 (m-10) cc_final: 0.5473 (m-90) REVERT: A 1021 MET cc_start: 0.7306 (tpp) cc_final: 0.6754 (tpp) REVERT: A 1045 PHE cc_start: 0.9069 (t80) cc_final: 0.8826 (t80) REVERT: A 1089 MET cc_start: 0.8767 (mtm) cc_final: 0.8175 (ttm) REVERT: A 1164 LEU cc_start: 0.8736 (tp) cc_final: 0.8470 (tt) REVERT: A 1313 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: C 7 LYS cc_start: 0.8556 (ptmm) cc_final: 0.8211 (ptmm) REVERT: C 96 GLU cc_start: 0.8670 (tp30) cc_final: 0.8418 (tm-30) REVERT: C 120 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8937 (tp) outliers start: 42 outliers final: 29 residues processed: 190 average time/residue: 0.2366 time to fit residues: 69.4188 Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1297 HIS Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 0.0070 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14682 Z= 0.154 Angle : 0.655 15.361 20435 Z= 0.314 Chirality : 0.039 0.319 2411 Planarity : 0.003 0.037 2194 Dihedral : 18.841 177.882 3378 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.81 % Allowed : 21.34 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.05 (0.22), residues: 1490 helix: 0.49 (0.22), residues: 627 sheet: -0.97 (0.49), residues: 113 loop : -1.72 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1074 HIS 0.009 0.001 HIS A 511 PHE 0.023 0.001 PHE A 916 TYR 0.022 0.001 TYR A 988 ARG 0.006 0.000 ARG C 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2980 Ramachandran restraints generated. 1490 Oldfield, 0 Emsley, 1490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7710 (tt) REVERT: A 241 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 396 GLU cc_start: 0.8471 (tp30) cc_final: 0.8126 (tp30) REVERT: A 618 ASP cc_start: 0.8830 (p0) cc_final: 0.8518 (p0) REVERT: A 712 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7951 (mm110) REVERT: A 727 LEU cc_start: 0.8934 (mp) cc_final: 0.8715 (mt) REVERT: A 759 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8649 (pp) REVERT: A 1045 PHE cc_start: 0.8917 (t80) cc_final: 0.8630 (t80) REVERT: A 1089 MET cc_start: 0.8798 (mtm) cc_final: 0.8168 (ttm) REVERT: C 7 LYS cc_start: 0.8476 (ptmm) cc_final: 0.8138 (ptmm) REVERT: C 96 GLU cc_start: 0.8708 (tp30) cc_final: 0.8441 (tm-30) REVERT: C 120 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8916 (tp) outliers start: 34 outliers final: 25 residues processed: 179 average time/residue: 0.2417 time to fit residues: 67.2222 Evaluate side-chains 180 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1297 HIS Chi-restraints excluded: chain A residue 1311 HIS Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 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 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.135847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101125 restraints weight = 29093.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103908 restraints weight = 16107.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104525 restraints weight = 10271.281| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14682 Z= 0.263 Angle : 0.709 15.069 20435 Z= 0.350 Chirality : 0.043 0.358 2411 Planarity : 0.004 0.043 2194 Dihedral : 18.862 176.936 3378 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.23 % Allowed : 21.67 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -1.21 (0.22), residues: 1490 helix: 0.33 (0.21), residues: 637 sheet: -0.66 (0.53), residues: 95 loop : -1.87 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP A 883 HIS 0.012 0.002 HIS A 511 PHE 0.054 0.002 PHE A1008 TYR 0.032 0.002 TYR A1356 ARG 0.007 0.000 ARG C 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.44 seconds wall clock time: 49 minutes 20.45 seconds (2960.45 seconds total)