Starting phenix.real_space_refine on Sat Sep 12 07:09:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mcc_9067/09_2026/6mcc_9067.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: {'ASP:plan': 7, 'GLU:plan': 20, 'ARG:plan': 12, 'PHE:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 7, 'TYR:plan': 2} 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, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 2.59, per 1000 atoms: 0.18 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: 1.06 Conformation dependent library (CDL) restraints added in 455.3 milliseconds 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: 1.70 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: 2.51 Time building geometry restraints manager: 1.36 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: 19559 2.54 - 5.08: 760 5.08 - 7.62: 90 7.62 - 10.16: 19 10.16 - 12.69: 7 Bond angle restraints: 20435 Sorted by residual: angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 119.70 126.65 -6.95 1.20e+00 6.94e-01 3.35e+01 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 ... (remaining 20430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8234 35.47 - 70.95: 346 70.95 - 106.42: 19 106.42 - 141.90: 1 141.90 - 177.37: 2 Dihedral angle restraints: 8602 sinusoidal: 4201 harmonic: 4401 Sorted by residual: dihedral pdb=" C4' A B 47 " pdb=" C3' A B 47 " pdb=" C2' A B 47 " pdb=" C1' A B 47 " ideal model delta sinusoidal sigma weight residual 36.34 -41.17 77.51 1 3.10e+00 1.04e-01 7.83e+02 dihedral pdb=" C4' A B 8 " pdb=" C3' A B 8 " pdb=" C2' A B 8 " pdb=" C1' A B 8 " ideal model delta sinusoidal sigma weight residual 36.34 -40.67 77.02 1 3.10e+00 1.04e-01 7.75e+02 dihedral pdb=" C4' G B 11 " pdb=" C3' G B 11 " pdb=" C2' G B 11 " pdb=" C1' G B 11 " ideal model delta sinusoidal sigma weight residual 36.34 -38.85 75.19 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 8599 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=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.50 -2.91 0.41 2.00e-01 2.50e+01 4.14e+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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 14683 Z= 0.305 Angle : 1.113 12.694 20435 Z= 0.549 Chirality : 0.160 4.814 2411 Planarity : 0.006 0.052 2194 Dihedral : 16.647 177.369 5754 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.022 0.001 ARG A 78 TYR 0.023 0.003 TYR A 72 PHE 0.044 0.003 PHE A1008 TRP 0.042 0.003 TRP A 476 HIS 0.009 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 (14682) covalent geometry : angle 1.11343 / 0.55 (20435) hydrogen bonds : bond 0.17404 / 8.99 ( 513) hydrogen bonds : angle 7.67069 / 3.05 ( 1406) Misc. bond : bond 0.04333 / 2.17 ( 1) *********************** 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 : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8879 (p-90) cc_final: 0.8611 (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: 0.7772 (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: 0.1112 time to fit residues: 41.1342 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 : 0.476 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 412 HIS A 489 GLN A 522 ASN A 739 GLN A 831 ASN A 930 HIS A 980 ASN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1054 ASN A1093 ASN A1101 GLN A1297 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.136840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096496 restraints weight = 30891.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100119 restraints weight = 16283.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.102483 restraints weight = 10984.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103920 restraints weight = 8602.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.104898 restraints weight = 7431.435| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14683 Z= 0.230 Angle : 0.991 14.426 20435 Z= 0.443 Chirality : 0.077 1.192 2411 Planarity : 0.005 0.051 2194 Dihedral : 16.482 173.781 3018 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.72 % Allowed : 13.65 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.19), residues: 1490 helix: -1.77 (0.18), residues: 623 sheet: -1.51 (0.46), residues: 109 loop : -2.69 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.020 0.002 TYR A1356 PHE 0.033 0.002 PHE A1008 TRP 0.019 0.002 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (14682) covalent geometry : angle 0.99119 / 0.44 (20435) hydrogen bonds : bond 0.05442 / 2.82 ( 513) hydrogen bonds : angle 5.25664 / 2.15 ( 1406) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** 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 212 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8905 (p-90) cc_final: 0.8198 (p-90) REVERT: A 64 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8464 (tm) REVERT: A 152 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8161 (ptt90) REVERT: A 238 PHE cc_start: 0.8305 (t80) cc_final: 0.7926 (t80) REVERT: A 465 MET cc_start: 0.7789 (ppp) cc_final: 0.7391 (ppp) REVERT: A 585 ASP cc_start: 0.8045 (p0) cc_final: 0.7520 (p0) REVERT: A 586 ARG cc_start: 0.8631 (mtm110) cc_final: 0.8425 (mtm-85) REVERT: A 684 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7898 (tttt) REVERT: A 706 GLU cc_start: 0.7891 (mp0) cc_final: 0.7640 (mp0) REVERT: A 761 ILE cc_start: 0.9006 (pp) cc_final: 0.8521 (pp) REVERT: A 762 GLU cc_start: 0.7545 (pm20) cc_final: 0.7299 (pm20) REVERT: A 879 MET cc_start: 0.7782 (mtt) cc_final: 0.7211 (mtt) REVERT: A 1046 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: A 1118 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7989 (tttt) REVERT: A 1205 GLU cc_start: 0.8229 (tt0) cc_final: 0.7899 (tt0) REVERT: A 1225 GLU cc_start: 0.7946 (mp0) cc_final: 0.7625 (mp0) REVERT: A 1365 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8609 (tm) REVERT: C 25 ARG cc_start: 0.7902 (tmm-80) cc_final: 0.7560 (tmm-80) REVERT: C 39 TYR cc_start: 0.8650 (m-80) cc_final: 0.8419 (m-10) REVERT: C 120 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8802 (tp) outliers start: 45 outliers final: 17 residues processed: 202 average time/residue: 0.0985 time to fit residues: 30.4211 Evaluate side-chains 162 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 152 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 474 THR 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 958 LEU 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 7 LYS Chi-restraints excluded: chain C residue 74 THR 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 137 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** 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 = 0.4037 r_free = 0.4037 target = 0.131627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093312 restraints weight = 30951.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096678 restraints weight = 16126.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098896 restraints weight = 10877.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100147 restraints weight = 8524.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101122 restraints weight = 7403.282| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14683 Z= 0.281 Angle : 0.960 14.822 20435 Z= 0.437 Chirality : 0.069 0.796 2411 Planarity : 0.005 0.050 2194 Dihedral : 16.385 178.046 3018 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.21 % Allowed : 15.63 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.20), residues: 1490 helix: -1.21 (0.19), residues: 631 sheet: -1.38 (0.47), residues: 113 loop : -2.50 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.023 0.002 TYR A 988 PHE 0.032 0.002 PHE A1008 TRP 0.034 0.003 TRP A 476 HIS 0.009 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.28 (14682) covalent geometry : angle 0.95992 / 0.44 (20435) hydrogen bonds : bond 0.05752 / 2.96 ( 513) hydrogen bonds : angle 5.16376 / 2.10 ( 1406) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** 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 221 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 158 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8905 (p-90) cc_final: 0.8281 (p-90) REVERT: A 84 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7615 (tp30) REVERT: A 152 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8219 (ptt90) REVERT: A 241 LEU cc_start: 0.9042 (mm) cc_final: 0.8514 (pp) REVERT: A 465 MET cc_start: 0.8049 (ppp) cc_final: 0.7613 (ppp) REVERT: A 585 ASP cc_start: 0.7880 (p0) cc_final: 0.7441 (p0) REVERT: A 586 ARG cc_start: 0.8525 (mtm110) cc_final: 0.8210 (mtm110) REVERT: A 684 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7954 (tttt) REVERT: A 706 GLU cc_start: 0.7896 (mp0) cc_final: 0.7448 (mp0) REVERT: A 759 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8829 (pp) REVERT: A 761 ILE cc_start: 0.9112 (pp) cc_final: 0.8827 (pp) REVERT: A 879 MET cc_start: 0.7492 (mtt) cc_final: 0.7058 (mtt) REVERT: A 920 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 1074 TRP cc_start: 0.5082 (t60) cc_final: 0.4496 (t60) REVERT: A 1118 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8108 (tttt) REVERT: A 1205 GLU cc_start: 0.8230 (tt0) cc_final: 0.8016 (tt0) REVERT: A 1276 PHE cc_start: 0.8411 (t80) cc_final: 0.7946 (t80) REVERT: A 1313 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: A 1365 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8562 (tm) REVERT: C 39 TYR cc_start: 0.8643 (m-80) cc_final: 0.8439 (m-10) REVERT: C 97 ASP cc_start: 0.8017 (t0) cc_final: 0.7507 (t70) REVERT: C 120 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8902 (tp) outliers start: 63 outliers final: 31 residues processed: 203 average time/residue: 0.0944 time to fit residues: 30.1252 Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 152 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 353 ASP 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 474 THR 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 786 GLU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 958 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 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 57 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 105 LEU 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 121 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100766 restraints weight = 30124.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.104391 restraints weight = 15238.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106781 restraints weight = 10050.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.108288 restraints weight = 7758.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109268 restraints weight = 6610.858| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14683 Z= 0.132 Angle : 0.812 14.458 20435 Z= 0.359 Chirality : 0.058 0.624 2411 Planarity : 0.003 0.045 2194 Dihedral : 16.011 176.204 3018 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.22 % Allowed : 16.87 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.21), residues: 1490 helix: -0.46 (0.20), residues: 626 sheet: -1.13 (0.48), residues: 113 loop : -2.26 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.023 0.001 TYR A 988 PHE 0.030 0.001 PHE A1008 TRP 0.016 0.002 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14682) covalent geometry : angle 0.81181 / 0.36 (20435) hydrogen bonds : bond 0.04267 / 2.20 ( 513) hydrogen bonds : angle 4.59292 / 1.88 ( 1406) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** 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 225 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8785 (p-90) cc_final: 0.8164 (p-90) REVERT: A 64 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8315 (tm) REVERT: A 241 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8609 (pp) REVERT: A 422 ILE cc_start: 0.9537 (tp) cc_final: 0.9239 (tp) REVERT: A 684 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7959 (tttt) REVERT: A 706 GLU cc_start: 0.7774 (mp0) cc_final: 0.7292 (mp0) REVERT: A 761 ILE cc_start: 0.9175 (pp) cc_final: 0.8791 (pp) REVERT: A 879 MET cc_start: 0.7762 (mtt) cc_final: 0.7491 (mtt) REVERT: A 883 TRP cc_start: 0.5902 (m-10) cc_final: 0.5595 (m-90) REVERT: A 920 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 1021 MET cc_start: 0.7674 (tpp) cc_final: 0.6821 (tpp) REVERT: A 1046 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 1168 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 1205 GLU cc_start: 0.8146 (tt0) cc_final: 0.7892 (tt0) REVERT: A 1313 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: A 1365 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8500 (tm) REVERT: C 100 GLU cc_start: 0.8533 (mp0) cc_final: 0.8306 (mp0) REVERT: C 120 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8845 (tp) outliers start: 51 outliers final: 24 residues processed: 208 average time/residue: 0.0881 time to fit residues: 28.7827 Evaluate side-chains 172 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 158 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 255 ASN 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 482 VAL 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 760 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 1280 VAL 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 57 VAL Chi-restraints excluded: chain C residue 105 LEU 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 11 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 985 HIS ** 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 = 0.4069 r_free = 0.4069 target = 0.133951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095115 restraints weight = 30948.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098411 restraints weight = 16659.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100548 restraints weight = 11419.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101933 restraints weight = 9047.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.102773 restraints weight = 7853.463| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14683 Z= 0.227 Angle : 0.885 13.546 20435 Z= 0.397 Chirality : 0.063 0.668 2411 Planarity : 0.004 0.049 2194 Dihedral : 16.019 176.977 3018 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.96 % Allowed : 18.78 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.21), residues: 1490 helix: -0.38 (0.21), residues: 627 sheet: -1.28 (0.48), residues: 113 loop : -2.23 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.020 0.002 TYR A 988 PHE 0.030 0.002 PHE A 238 TRP 0.033 0.003 TRP A1074 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (14682) covalent geometry : angle 0.88481 / 0.40 (20435) hydrogen bonds : bond 0.05189 / 2.66 ( 513) hydrogen bonds : angle 4.77816 / 1.95 ( 1406) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** 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 216 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 TRP cc_start: 0.8816 (p-90) cc_final: 0.8148 (p-90) REVERT: A 152 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8555 (ptt90) REVERT: A 241 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 712 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7710 (mm110) REVERT: A 738 LEU cc_start: 0.8342 (tt) cc_final: 0.7688 (mt) REVERT: A 879 MET cc_start: 0.7809 (mtt) cc_final: 0.7432 (mtt) REVERT: A 883 TRP cc_start: 0.5929 (m-10) cc_final: 0.5588 (m-90) REVERT: A 1021 MET cc_start: 0.7727 (tpp) cc_final: 0.6876 (tpp) REVERT: A 1043 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (tpp) REVERT: A 1205 GLU cc_start: 0.8171 (tt0) cc_final: 0.7963 (tt0) REVERT: A 1313 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6916 (m-10) REVERT: C 97 ASP cc_start: 0.7758 (t0) cc_final: 0.7244 (t0) REVERT: C 100 GLU cc_start: 0.8522 (mp0) cc_final: 0.8286 (mp0) REVERT: C 120 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8853 (tp) outliers start: 60 outliers final: 31 residues processed: 196 average time/residue: 0.0925 time to fit residues: 28.9489 Evaluate side-chains 173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 152 ARG Chi-restraints excluded: chain A residue 158 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 254 SER Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 269 ASP 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 591 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1050 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 1238 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 105 LEU 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 6 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 5 optimal weight: 10.0000 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** 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 = 0.136825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098760 restraints weight = 30121.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102059 restraints weight = 16334.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104337 restraints weight = 11204.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105718 restraints weight = 8801.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106499 restraints weight = 7616.285| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14683 Z= 0.139 Angle : 0.809 13.489 20435 Z= 0.357 Chirality : 0.057 0.634 2411 Planarity : 0.003 0.045 2194 Dihedral : 15.775 174.568 3018 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.30 % Allowed : 19.77 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1490 helix: -0.05 (0.21), residues: 627 sheet: -1.19 (0.48), residues: 113 loop : -2.03 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.022 0.001 TYR A 988 PHE 0.036 0.001 PHE A1008 TRP 0.015 0.002 TRP A1074 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14682) covalent geometry : angle 0.80857 / 0.36 (20435) hydrogen bonds : bond 0.04338 / 2.23 ( 513) hydrogen bonds : angle 4.52156 / 1.84 ( 1406) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** 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 217 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 165 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8421 (tm) REVERT: A 241 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 662 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 879 MET cc_start: 0.7995 (mtt) cc_final: 0.7705 (mtt) REVERT: A 883 TRP cc_start: 0.5877 (m-10) cc_final: 0.5608 (m-90) REVERT: A 1021 MET cc_start: 0.7753 (tpp) cc_final: 0.6915 (tpp) REVERT: A 1043 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8476 (mmm) REVERT: A 1205 GLU cc_start: 0.8116 (tt0) cc_final: 0.7878 (tt0) REVERT: A 1313 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: C 97 ASP cc_start: 0.7950 (t0) cc_final: 0.7407 (t0) REVERT: C 100 GLU cc_start: 0.8376 (mp0) cc_final: 0.8144 (mp0) REVERT: C 120 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8856 (tp) outliers start: 52 outliers final: 28 residues processed: 200 average time/residue: 0.0978 time to fit residues: 30.7670 Evaluate side-chains 177 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 158 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 255 ASN 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 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 639 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1203 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 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 985 HIS ** 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 = 0.4033 r_free = 0.4033 target = 0.132307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093726 restraints weight = 30251.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.097042 restraints weight = 16210.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099219 restraints weight = 10980.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.100630 restraints weight = 8672.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101407 restraints weight = 7481.054| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14683 Z= 0.236 Angle : 0.894 15.025 20435 Z= 0.402 Chirality : 0.062 0.656 2411 Planarity : 0.004 0.048 2194 Dihedral : 15.875 174.146 3018 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.21 % Allowed : 19.52 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.22), residues: 1490 helix: -0.16 (0.21), residues: 625 sheet: -1.23 (0.47), residues: 115 loop : -2.03 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 25 TYR 0.020 0.002 TYR A 988 PHE 0.016 0.002 PHE A 375 TRP 0.016 0.002 TRP A 476 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (14682) covalent geometry : angle 0.89384 / 0.40 (20435) hydrogen bonds : bond 0.05244 / 2.69 ( 513) hydrogen bonds : angle 4.79110 / 1.93 ( 1406) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** 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 203 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 241 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 662 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 712 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7826 (mm110) REVERT: A 879 MET cc_start: 0.7869 (mtt) cc_final: 0.7508 (mtt) REVERT: A 883 TRP cc_start: 0.5850 (m-10) cc_final: 0.5459 (m-90) REVERT: A 1021 MET cc_start: 0.7756 (tpp) cc_final: 0.7175 (tpp) REVERT: A 1043 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8273 (tpp) REVERT: A 1089 MET cc_start: 0.8698 (ttt) cc_final: 0.8333 (ttt) REVERT: A 1205 GLU cc_start: 0.8196 (tt0) cc_final: 0.7952 (tt0) REVERT: A 1313 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7031 (m-10) REVERT: A 1350 GLN cc_start: 0.8142 (tt0) cc_final: 0.7905 (tt0) REVERT: C 96 GLU cc_start: 0.8459 (tp30) cc_final: 0.8175 (tm-30) REVERT: C 97 ASP cc_start: 0.8111 (t0) cc_final: 0.7607 (t0) REVERT: C 100 GLU cc_start: 0.8500 (mp0) cc_final: 0.8205 (mp0) outliers start: 63 outliers final: 37 residues processed: 184 average time/residue: 0.0967 time to fit residues: 28.7856 Evaluate side-chains 181 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 158 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 242 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 255 ASN 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 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 712 GLN Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1106 SER 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 1238 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 A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.138216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100255 restraints weight = 30226.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103672 restraints weight = 16424.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105909 restraints weight = 11190.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107400 restraints weight = 8809.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108205 restraints weight = 7563.538| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14683 Z= 0.127 Angle : 0.814 16.476 20435 Z= 0.359 Chirality : 0.056 0.602 2411 Planarity : 0.003 0.043 2194 Dihedral : 15.581 170.081 3018 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.06 % Allowed : 21.67 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.22), residues: 1490 helix: 0.14 (0.21), residues: 622 sheet: -1.07 (0.48), residues: 113 loop : -1.86 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.023 0.001 TYR A 988 PHE 0.021 0.001 PHE A1046 TRP 0.037 0.003 TRP A1074 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (14682) covalent geometry : angle 0.81435 / 0.36 (20435) hydrogen bonds : bond 0.04197 / 2.16 ( 513) hydrogen bonds : angle 4.46624 / 1.81 ( 1406) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** 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 208 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8440 (tm) REVERT: A 169 LEU cc_start: 0.8838 (mt) cc_final: 0.8606 (mp) REVERT: A 241 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8696 (pp) REVERT: A 403 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8404 (mtp85) REVERT: A 662 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8533 (pp) REVERT: A 712 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7654 (mm110) REVERT: A 879 MET cc_start: 0.8062 (mtt) cc_final: 0.7854 (mtt) REVERT: A 1021 MET cc_start: 0.7617 (tpp) cc_final: 0.7086 (tpp) REVERT: A 1089 MET cc_start: 0.8659 (ttt) cc_final: 0.8290 (ttt) REVERT: A 1313 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: A 1350 GLN cc_start: 0.8067 (tt0) cc_final: 0.7831 (tt0) REVERT: C 7 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8199 (ptmm) REVERT: C 35 ASN cc_start: 0.8797 (m110) cc_final: 0.8592 (m-40) REVERT: C 96 GLU cc_start: 0.8450 (tp30) cc_final: 0.8177 (tm-30) REVERT: C 97 ASP cc_start: 0.8015 (t0) cc_final: 0.7555 (t0) REVERT: C 100 GLU cc_start: 0.8420 (mp0) cc_final: 0.8121 (mp0) outliers start: 37 outliers final: 26 residues processed: 194 average time/residue: 0.1000 time to fit residues: 30.5360 Evaluate side-chains 189 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 158 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 255 ASN 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 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 639 TYR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1198 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 A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 33 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.131356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092460 restraints weight = 30660.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095725 restraints weight = 16550.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097911 restraints weight = 11359.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099312 restraints weight = 8981.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099947 restraints weight = 7769.641| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14683 Z= 0.286 Angle : 0.944 15.499 20435 Z= 0.428 Chirality : 0.064 0.649 2411 Planarity : 0.004 0.050 2194 Dihedral : 15.799 167.895 3018 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.72 % Allowed : 21.34 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1490 helix: -0.13 (0.21), residues: 622 sheet: -1.11 (0.49), residues: 115 loop : -2.03 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 25 TYR 0.020 0.002 TYR A 988 PHE 0.020 0.002 PHE A 375 TRP 0.058 0.006 TRP A1074 HIS 0.030 0.002 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (14682) covalent geometry : angle 0.94427 / 0.43 (20435) hydrogen bonds : bond 0.05540 / 2.84 ( 513) hydrogen bonds : angle 4.93016 / 1.98 ( 1406) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** 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 189 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 241 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 662 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 712 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7781 (mm110) REVERT: A 760 VAL cc_start: 0.9551 (OUTLIER) cc_final: 0.9237 (p) REVERT: A 879 MET cc_start: 0.8204 (mtt) cc_final: 0.7930 (mtt) REVERT: A 1000 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8247 (tptt) REVERT: A 1021 MET cc_start: 0.7701 (tpp) cc_final: 0.7376 (tpp) REVERT: A 1089 MET cc_start: 0.8688 (ttt) cc_final: 0.8325 (ttt) REVERT: A 1313 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7038 (m-10) REVERT: C 96 GLU cc_start: 0.8541 (tp30) cc_final: 0.8271 (tm-30) REVERT: C 97 ASP cc_start: 0.8204 (t0) cc_final: 0.7852 (t70) REVERT: C 100 GLU cc_start: 0.8519 (mp0) cc_final: 0.8211 (mp0) outliers start: 45 outliers final: 30 residues processed: 174 average time/residue: 0.0958 time to fit residues: 26.6334 Evaluate side-chains 175 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 142 LEU Chi-restraints excluded: chain A residue 158 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 242 ILE 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 466 THR 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 712 GLN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 958 LEU 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 1198 LEU Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1280 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097845 restraints weight = 30099.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101161 restraints weight = 16484.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103356 restraints weight = 11307.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104646 restraints weight = 8936.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105649 restraints weight = 7750.180| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14683 Z= 0.156 Angle : 0.849 15.750 20435 Z= 0.378 Chirality : 0.058 0.586 2411 Planarity : 0.004 0.044 2194 Dihedral : 15.580 166.028 3018 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.06 % Allowed : 22.25 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.22), residues: 1490 helix: 0.06 (0.21), residues: 626 sheet: -1.12 (0.49), residues: 115 loop : -1.91 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.023 0.001 TYR A 988 PHE 0.033 0.001 PHE A1008 TRP 0.036 0.003 TRP A1074 HIS 0.017 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (14682) covalent geometry : angle 0.84912 / 0.38 (20435) hydrogen bonds : bond 0.04600 / 2.36 ( 513) hydrogen bonds : angle 4.61456 / 1.87 ( 1406) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** 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 189 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8709 (pp) REVERT: A 403 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8391 (mtp85) REVERT: A 662 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 712 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7775 (mm110) REVERT: A 879 MET cc_start: 0.8140 (mtt) cc_final: 0.7899 (mtt) REVERT: A 1021 MET cc_start: 0.7562 (tpp) cc_final: 0.7328 (tpp) REVERT: A 1089 MET cc_start: 0.8607 (ttt) cc_final: 0.8296 (ttt) REVERT: A 1313 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6934 (m-10) REVERT: C 97 ASP cc_start: 0.8077 (t0) cc_final: 0.7604 (t0) REVERT: C 100 GLU cc_start: 0.8373 (mp0) cc_final: 0.8081 (mp0) outliers start: 37 outliers final: 26 residues processed: 176 average time/residue: 0.1006 time to fit residues: 28.1906 Evaluate side-chains 174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 158 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 254 SER 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 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 662 LEU Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 958 LEU 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 1198 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 A residue 1365 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 GLN A 930 HIS ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.134780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096364 restraints weight = 30322.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099673 restraints weight = 16396.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.101880 restraints weight = 11264.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.103256 restraints weight = 8905.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104210 restraints weight = 7696.757| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14683 Z= 0.183 Angle : 0.865 15.553 20435 Z= 0.387 Chirality : 0.058 0.565 2411 Planarity : 0.004 0.045 2194 Dihedral : 15.553 165.951 3018 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.39 % Allowed : 22.50 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.22), residues: 1490 helix: 0.08 (0.21), residues: 626 sheet: -1.13 (0.49), residues: 115 loop : -1.88 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 25 TYR 0.023 0.002 TYR A 988 PHE 0.014 0.001 PHE A 446 TRP 0.038 0.003 TRP A1074 HIS 0.019 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (14682) covalent geometry : angle 0.86483 / 0.39 (20435) hydrogen bonds : bond 0.04878 / 2.50 ( 513) hydrogen bonds : angle 4.65511 / 1.88 ( 1406) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.96 seconds wall clock time: 40 minutes 32.59 seconds (2432.59 seconds total)