Starting phenix.real_space_refine on Sat Sep 12 06:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vzl_8749/09_2026/5vzl_8749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vzl_8749/09_2026/5vzl_8749.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/5vzl_8749/09_2026/5vzl_8749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2026/5vzl_8749_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2026/5vzl_8749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vzl_8749/09_2026/5vzl_8749.map" } 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= 0.000 sd= 0.005 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 25 5.16 5 C 8364 2.51 5 N 2420 2.21 5 O 2988 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: 13915 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10711 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 21, 'ARG:plan': 10, 'PHE:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 220 Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 13915 At special positions: 0 Unit cell: (112.35, 136.96, 120.91, 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 25 16.00 P 118 15.00 O 2988 8.00 N 2420 7.00 C 8364 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: 0.94 Conformation dependent library (CDL) restraints added in 557.2 milliseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 11 sheets defined 52.0% alpha, 6.6% beta 30 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.556A pdb=" N ARG A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.739A pdb=" N MET A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.866A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.768A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.807A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.865A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.859A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 5.253A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 282 No H-bonds generated for 'chain 'A' and resid 281 through 282' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.506A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.816A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.314A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.709A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.632A pdb=" N VAL A 481 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 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 603 through 608 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.904A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 removed outlier: 4.328A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.860A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.579A pdb=" N HIS A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.898A pdb=" N LYS A 772 " --> pdb=" O THR A 769 " (cutoff:3.500A) removed outlier: 3.976A 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 776 through 792 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.620A pdb=" N LYS A 797 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.613A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.593A pdb=" N ARG A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.708A pdb=" N LYS A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.834A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.592A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.822A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.767A pdb=" N GLU A1007 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 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 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.850A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 3.974A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A1279 " --> pdb=" O GLU A1275 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A1280 " --> pdb=" O PHE A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.609A 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 1317 Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.627A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.934A pdb=" N LEU C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.999A pdb=" N LEU C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.597A 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: 6.178A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1050 through 1051 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.267A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.564A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A1166 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.796A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.938A pdb=" N ILE C 43 " --> pdb=" O LEU C 30 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.33 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: 2283 1.32 - 1.44: 4269 1.44 - 1.56: 7579 1.56 - 1.69: 234 1.69 - 1.81: 48 Bond restraints: 14413 Sorted by residual: bond pdb=" N9 A B 6 " pdb=" C4 A B 6 " ideal model delta sigma weight residual 1.374 1.399 -0.025 6.00e-03 2.78e+04 1.67e+01 bond pdb=" N9 G B 4 " pdb=" C4 G B 4 " ideal model delta sigma weight residual 1.375 1.405 -0.030 8.00e-03 1.56e+04 1.45e+01 bond pdb=" C6 G B 76 " pdb=" N1 G B 76 " ideal model delta sigma weight residual 1.391 1.369 0.022 7.00e-03 2.04e+04 9.55e+00 bond pdb=" N9 A B 49 " pdb=" C4 A B 49 " ideal model delta sigma weight residual 1.374 1.357 0.017 6.00e-03 2.78e+04 8.43e+00 bond pdb=" N9 A B 47 " pdb=" C4 A B 47 " ideal model delta sigma weight residual 1.374 1.359 0.015 6.00e-03 2.78e+04 6.15e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19388 2.48 - 4.96: 588 4.96 - 7.43: 65 7.43 - 9.91: 15 9.91 - 12.39: 3 Bond angle restraints: 20059 Sorted by residual: angle pdb=" C1' G B 4 " pdb=" N9 G B 4 " pdb=" C4 G B 4 " ideal model delta sigma weight residual 126.50 136.70 -10.20 1.30e+00 5.92e-01 6.16e+01 angle pdb=" N9 G B 4 " pdb=" C4 G B 4 " pdb=" N3 G B 4 " ideal model delta sigma weight residual 126.00 130.66 -4.66 6.00e-01 2.78e+00 6.03e+01 angle pdb=" C5 G B 4 " pdb=" C4 G B 4 " pdb=" N3 G B 4 " ideal model delta sigma weight residual 128.60 124.81 3.79 5.00e-01 4.00e+00 5.75e+01 angle pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sigma weight residual 118.80 126.56 -7.76 1.10e+00 8.26e-01 4.98e+01 angle pdb=" N1 C B 20 " pdb=" C2 C B 20 " pdb=" O2 C B 20 " ideal model delta sigma weight residual 118.90 123.08 -4.18 6.00e-01 2.78e+00 4.87e+01 ... (remaining 20054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8449 35.20 - 70.39: 317 70.39 - 105.59: 37 105.59 - 140.78: 4 140.78 - 175.98: 5 Dihedral angle restraints: 8812 sinusoidal: 4546 harmonic: 4266 Sorted by residual: dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 39.82 160.18 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U B 7 " pdb=" C1' U B 7 " pdb=" N1 U B 7 " pdb=" C2 U B 7 " ideal model delta sinusoidal sigma weight residual 232.00 56.02 175.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N GLU C 47 " pdb=" CA GLU C 47 " ideal model delta harmonic sigma weight residual 180.00 143.46 36.54 0 5.00e+00 4.00e-02 5.34e+01 ... (remaining 8809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1807 0.062 - 0.125: 451 0.125 - 0.187: 88 0.187 - 0.250: 8 0.250 - 0.312: 2 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C3' C B 35 " pdb=" C4' C B 35 " pdb=" O3' C B 35 " pdb=" C2' C B 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' A B 47 " pdb=" C4' A B 47 " pdb=" O3' A B 47 " pdb=" C2' A B 47 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' A B 45 " pdb=" O4' A B 45 " pdb=" C2' A B 45 " pdb=" N9 A B 45 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2353 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 47 " 0.040 2.00e-02 2.50e+03 1.79e-02 8.80e+00 pdb=" N9 A B 47 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A B 47 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 47 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 47 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B 47 " 0.013 2.00e-02 2.50e+03 pdb=" C2 A B 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A B 47 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 47 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 271 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C TYR A 271 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR A 271 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 272 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1326 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C TYR A1326 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A1326 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A1327 " 0.016 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2067 2.75 - 3.29: 13382 3.29 - 3.83: 24507 3.83 - 4.36: 27918 4.36 - 4.90: 42797 Nonbonded interactions: 110671 Sorted by model distance: nonbonded pdb=" O2' G B 61 " pdb=" OH TYR A 359 " model vdw 2.216 3.040 nonbonded pdb=" O GLN C 78 " pdb=" OG1 THR C 81 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR A 560 " pdb=" OD1 ASP A 585 " model vdw 2.296 3.040 ... (remaining 110666 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0326 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 0.098 14414 Z= 0.385 Angle : 1.005 12.390 20059 Z= 0.715 Chirality : 0.057 0.312 2356 Planarity : 0.006 0.068 2153 Dihedral : 17.273 175.978 6052 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.25 % Allowed : 3.33 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -4.13 (0.17), residues: 1447 helix: -2.93 (0.14), residues: 661 sheet: -1.64 (0.49), residues: 110 loop : -2.64 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 78 TYR 0.028 0.003 TYR A 973 PHE 0.020 0.003 PHE A1008 TRP 0.011 0.003 TRP A 464 HIS 0.007 0.002 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.38 (14413) covalent geometry : angle 1.00518 / 0.72 (20059) hydrogen bonds : bond 0.15738 / 16.78 ( 567) hydrogen bonds : angle 9.97298 / 12.89 ( 1540) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: -0.3469 (OUTLIER) cc_final: -0.3745 (mpt-90) REVERT: A 642 LEU cc_start: 0.3241 (mm) cc_final: 0.2945 (mm) REVERT: A 643 PHE cc_start: 0.0746 (m-10) cc_final: 0.0429 (m-80) REVERT: A 822 MET cc_start: -0.4326 (mmm) cc_final: -0.5093 (mtt) REVERT: A 1213 MET cc_start: 0.4589 (mtm) cc_final: 0.4065 (ppp) outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.1482 time to fit residues: 25.9781 Evaluate side-chains 82 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 137 HIS A 194 GLN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A 522 ASN A 595 HIS ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A 767 ASN A 863 ASN A 899 ASN A1286 ASN A1317 ASN C 2 ASN C 12 ASN C 25 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.266627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.226259 restraints weight = 28213.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.231207 restraints weight = 15432.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.234492 restraints weight = 9934.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.236647 restraints weight = 7255.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.237901 restraints weight = 5844.296| |-----------------------------------------------------------------------------| r_work (final): 0.4834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0528 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14414 Z= 0.156 Angle : 0.674 14.321 20059 Z= 0.359 Chirality : 0.042 0.337 2356 Planarity : 0.005 0.062 2153 Dihedral : 20.180 179.329 3330 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.42 % Allowed : 6.67 % Favored : 91.92 % 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: -2.71 (0.20), residues: 1447 helix: -1.24 (0.17), residues: 675 sheet: -1.75 (0.43), residues: 121 loop : -2.35 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.017 0.002 TYR A1326 PHE 0.014 0.002 PHE A 119 TRP 0.008 0.001 TRP A1126 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (14413) covalent geometry : angle 0.67390 / 0.36 (20059) hydrogen bonds : bond 0.05204 / 5.21 ( 567) hydrogen bonds : angle 6.15984 / 7.71 ( 1540) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 119 PHE cc_start: -0.0491 (m-10) cc_final: -0.1420 (m-10) REVERT: A 161 MET cc_start: 0.1860 (mmm) cc_final: 0.1521 (mmm) REVERT: A 194 GLN cc_start: -0.2651 (OUTLIER) cc_final: -0.3398 (mm-40) REVERT: A 631 MET cc_start: -0.2339 (mmm) cc_final: -0.2780 (mmm) REVERT: A 694 MET cc_start: -0.0963 (ppp) cc_final: -0.2285 (mpp) REVERT: A 822 MET cc_start: -0.2114 (mmm) cc_final: -0.3319 (mtt) REVERT: A 1089 MET cc_start: 0.1528 (tmm) cc_final: 0.1319 (tmm) REVERT: C 28 THR cc_start: 0.0509 (OUTLIER) cc_final: -0.0117 (m) REVERT: C 31 ILE cc_start: 0.3471 (OUTLIER) cc_final: 0.3223 (pp) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.1257 time to fit residues: 18.9372 Evaluate side-chains 86 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 127 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 609 ASN A 612 ASN A 709 GLN A 807 GLN A1264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.265960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.225886 restraints weight = 28790.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.230983 restraints weight = 15556.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.234405 restraints weight = 9932.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.236633 restraints weight = 7182.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.238163 restraints weight = 5733.687| |-----------------------------------------------------------------------------| r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0722 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14414 Z= 0.138 Angle : 0.606 13.792 20059 Z= 0.323 Chirality : 0.040 0.293 2356 Planarity : 0.005 0.090 2153 Dihedral : 19.920 179.603 3326 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.92 % Allowed : 7.50 % Favored : 90.58 % 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: -1.95 (0.20), residues: 1447 helix: -0.50 (0.18), residues: 688 sheet: -1.52 (0.45), residues: 118 loop : -2.11 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 557 TYR 0.018 0.002 TYR C 41 PHE 0.026 0.002 PHE A 491 TRP 0.009 0.001 TRP A 476 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (14413) covalent geometry : angle 0.60605 / 0.32 (20059) hydrogen bonds : bond 0.04589 / 4.60 ( 567) hydrogen bonds : angle 5.45896 / 6.85 ( 1540) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: -0.0613 (p) cc_final: -0.0887 (p) REVERT: A 119 PHE cc_start: -0.0936 (m-10) cc_final: -0.1573 (m-10) REVERT: A 241 LEU cc_start: -0.1772 (OUTLIER) cc_final: -0.2541 (mp) REVERT: A 694 MET cc_start: -0.0829 (ppp) cc_final: -0.2278 (mpp) REVERT: A 703 THR cc_start: 0.3009 (OUTLIER) cc_final: 0.2628 (t) REVERT: C 28 THR cc_start: 0.0475 (OUTLIER) cc_final: 0.0061 (m) REVERT: C 33 ARG cc_start: 0.4237 (mmt90) cc_final: 0.3789 (mmt90) outliers start: 23 outliers final: 13 residues processed: 106 average time/residue: 0.1248 time to fit residues: 19.6757 Evaluate side-chains 94 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 143 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 712 GLN A1264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.265236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.226508 restraints weight = 28487.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.231570 restraints weight = 15185.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.234870 restraints weight = 9570.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.237065 restraints weight = 6867.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 75)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.238521 restraints weight = 5462.264| |-----------------------------------------------------------------------------| r_work (final): 0.4847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0797 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14414 Z= 0.117 Angle : 0.564 17.792 20059 Z= 0.296 Chirality : 0.038 0.300 2356 Planarity : 0.004 0.047 2153 Dihedral : 19.743 179.974 3326 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.50 % Allowed : 8.75 % Favored : 89.75 % 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: -1.39 (0.21), residues: 1447 helix: 0.05 (0.19), residues: 689 sheet: -0.96 (0.48), residues: 101 loop : -1.98 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 400 TYR 0.025 0.002 TYR A 836 PHE 0.012 0.001 PHE A 491 TRP 0.008 0.001 TRP A 476 HIS 0.012 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (14413) covalent geometry : angle 0.56355 / 0.30 (20059) hydrogen bonds : bond 0.04094 / 4.14 ( 567) hydrogen bonds : angle 4.96980 / 6.25 ( 1540) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 THR cc_start: -0.0151 (p) cc_final: -0.0406 (p) REVERT: A 119 PHE cc_start: -0.0962 (m-10) cc_final: -0.1600 (m-10) REVERT: A 241 LEU cc_start: -0.1797 (OUTLIER) cc_final: -0.2569 (mp) REVERT: A 465 MET cc_start: -0.2738 (tpt) cc_final: -0.3026 (tpt) REVERT: A 694 MET cc_start: -0.0536 (ppp) cc_final: -0.1943 (mpp) REVERT: A 904 GLU cc_start: 0.4922 (tt0) cc_final: 0.3616 (mt-10) REVERT: A 976 ARG cc_start: 0.1990 (ptp-170) cc_final: -0.0125 (ptt-90) REVERT: C 31 ILE cc_start: 0.3912 (OUTLIER) cc_final: 0.3642 (pp) REVERT: C 33 ARG cc_start: 0.4384 (mmt90) cc_final: 0.3883 (mmt90) REVERT: C 77 MET cc_start: -0.0701 (mmp) cc_final: -0.1733 (ptt) REVERT: C 80 ILE cc_start: -0.2753 (OUTLIER) cc_final: -0.4021 (pt) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.1316 time to fit residues: 18.0321 Evaluate side-chains 85 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 80 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 224 ASN A 255 ASN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 920 GLN ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.265882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.227787 restraints weight = 29789.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.232756 restraints weight = 15926.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.235922 restraints weight = 10094.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.237903 restraints weight = 7326.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.239457 restraints weight = 5881.457| |-----------------------------------------------------------------------------| r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1574 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 14414 Z= 0.281 Angle : 1.011 25.741 20059 Z= 0.520 Chirality : 0.054 0.431 2356 Planarity : 0.007 0.075 2153 Dihedral : 20.118 174.003 3326 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.67 % Allowed : 10.58 % Favored : 86.75 % 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: -2.61 (0.19), residues: 1447 helix: -1.09 (0.18), residues: 702 sheet: -1.23 (0.45), residues: 101 loop : -2.53 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 221 TYR 0.033 0.004 TYR C 41 PHE 0.043 0.004 PHE A1324 TRP 0.026 0.004 TRP A 18 HIS 0.025 0.004 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.28 (14413) covalent geometry : angle 1.01113 / 0.52 (20059) hydrogen bonds : bond 0.07075 / 6.86 ( 567) hydrogen bonds : angle 5.94855 / 7.28 ( 1540) Misc. bond : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.433 Fit side-chains REVERT: A 194 GLN cc_start: -0.1530 (OUTLIER) cc_final: -0.2896 (mm-40) REVERT: A 241 LEU cc_start: -0.1445 (OUTLIER) cc_final: -0.2216 (mt) REVERT: A 418 GLU cc_start: -0.2195 (OUTLIER) cc_final: -0.3137 (pt0) REVERT: A 465 MET cc_start: -0.1850 (tpt) cc_final: -0.2106 (tpt) REVERT: A 631 MET cc_start: -0.1299 (mmm) cc_final: -0.1909 (mmm) REVERT: A 694 MET cc_start: 0.0388 (ppp) cc_final: -0.1904 (mpp) REVERT: A 904 GLU cc_start: 0.5820 (tt0) cc_final: 0.4401 (mt-10) REVERT: A 939 MET cc_start: -0.1932 (ptt) cc_final: -0.2440 (ptp) REVERT: A 970 PHE cc_start: 0.2704 (m-80) cc_final: 0.2393 (m-80) REVERT: A 976 ARG cc_start: 0.2539 (ptp-170) cc_final: 0.0225 (ptt-90) REVERT: A 1333 ARG cc_start: 0.0357 (OUTLIER) cc_final: -0.0861 (ptm160) REVERT: C 33 ARG cc_start: 0.4674 (mmt90) cc_final: 0.4387 (mmt90) REVERT: C 70 GLU cc_start: 0.0387 (OUTLIER) cc_final: 0.0069 (pt0) REVERT: C 71 GLU cc_start: -0.0757 (OUTLIER) cc_final: -0.1158 (pt0) outliers start: 32 outliers final: 14 residues processed: 115 average time/residue: 0.1197 time to fit residues: 20.6660 Evaluate side-chains 96 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1333 ARG Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 0.0570 chunk 79 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 224 ASN A 309 ASN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A1264 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.264655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.226449 restraints weight = 29188.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.231409 restraints weight = 15584.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.234589 restraints weight = 9814.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.236639 restraints weight = 7070.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.237800 restraints weight = 5664.918| |-----------------------------------------------------------------------------| r_work (final): 0.4863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1509 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14414 Z= 0.168 Angle : 0.693 10.959 20059 Z= 0.368 Chirality : 0.043 0.280 2356 Planarity : 0.005 0.059 2153 Dihedral : 19.891 176.344 3326 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.42 % Allowed : 12.42 % Favored : 85.17 % 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: -2.14 (0.20), residues: 1447 helix: -0.67 (0.18), residues: 684 sheet: -1.23 (0.50), residues: 87 loop : -2.24 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 221 TYR 0.018 0.002 TYR A 656 PHE 0.021 0.002 PHE A 682 TRP 0.018 0.002 TRP A 476 HIS 0.013 0.002 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (14413) covalent geometry : angle 0.69281 / 0.37 (20059) hydrogen bonds : bond 0.05159 / 5.16 ( 567) hydrogen bonds : angle 5.49302 / 6.80 ( 1540) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.416 Fit side-chains REVERT: A 201 ILE cc_start: -0.1765 (OUTLIER) cc_final: -0.2063 (pp) REVERT: A 241 LEU cc_start: -0.1569 (OUTLIER) cc_final: -0.2104 (mt) REVERT: A 373 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5702 (t80) REVERT: A 374 LYS cc_start: 0.6441 (tppt) cc_final: 0.6175 (tptm) REVERT: A 631 MET cc_start: -0.1661 (mmm) cc_final: -0.2327 (mmm) REVERT: A 694 MET cc_start: 0.0101 (ppp) cc_final: -0.1969 (mpp) REVERT: A 904 GLU cc_start: 0.5207 (tt0) cc_final: 0.3822 (mt-10) REVERT: A 970 PHE cc_start: 0.2739 (m-80) cc_final: 0.2494 (m-80) REVERT: A 976 ARG cc_start: 0.2872 (ptp-170) cc_final: 0.0059 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3065 (mtp85) cc_final: 0.2219 (mmm160) REVERT: C 79 THR cc_start: 0.3166 (OUTLIER) cc_final: 0.0636 (m) outliers start: 29 outliers final: 12 residues processed: 98 average time/residue: 0.1183 time to fit residues: 17.2073 Evaluate side-chains 85 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 111 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN A 985 HIS A1264 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.264184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.226814 restraints weight = 29122.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.231793 restraints weight = 15565.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.235039 restraints weight = 9824.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.237160 restraints weight = 7042.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.238458 restraints weight = 5606.742| |-----------------------------------------------------------------------------| r_work (final): 0.4875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1376 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14414 Z= 0.124 Angle : 0.604 10.578 20059 Z= 0.320 Chirality : 0.040 0.300 2356 Planarity : 0.004 0.051 2153 Dihedral : 19.668 176.949 3326 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.42 % Allowed : 13.83 % Favored : 84.75 % 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: 1447 helix: -0.16 (0.19), residues: 685 sheet: -1.39 (0.45), residues: 107 loop : -2.05 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1122 TYR 0.019 0.002 TYR A1356 PHE 0.024 0.002 PHE A 491 TRP 0.013 0.001 TRP A 476 HIS 0.007 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (14413) covalent geometry : angle 0.60360 / 0.32 (20059) hydrogen bonds : bond 0.04350 / 4.30 ( 567) hydrogen bonds : angle 5.02834 / 6.35 ( 1540) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.441 Fit side-chains REVERT: A 201 ILE cc_start: -0.2005 (OUTLIER) cc_final: -0.2279 (pp) REVERT: A 241 LEU cc_start: -0.2120 (OUTLIER) cc_final: -0.2724 (mt) REVERT: A 694 MET cc_start: 0.0115 (ppp) cc_final: -0.1882 (mpp) REVERT: A 904 GLU cc_start: 0.5391 (tt0) cc_final: 0.3885 (mt-10) REVERT: A 976 ARG cc_start: 0.2369 (ptp-170) cc_final: -0.0060 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3503 (mtp85) cc_final: 0.2432 (mmm160) REVERT: A 1169 MET cc_start: 0.2955 (mtt) cc_final: 0.2066 (mtm) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.1255 time to fit residues: 15.8019 Evaluate side-chains 79 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS ** A1317 ASN ** 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 = 0.5064 r_free = 0.5064 target = 0.264751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.227345 restraints weight = 29200.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.232226 restraints weight = 15736.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.235350 restraints weight = 9966.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.237539 restraints weight = 7229.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.238646 restraints weight = 5741.153| |-----------------------------------------------------------------------------| r_work (final): 0.4902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1365 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14414 Z= 0.122 Angle : 0.580 13.856 20059 Z= 0.307 Chirality : 0.040 0.361 2356 Planarity : 0.004 0.048 2153 Dihedral : 19.549 176.697 3326 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.50 % Allowed : 14.25 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.43 (0.21), residues: 1447 helix: 0.02 (0.20), residues: 687 sheet: -1.22 (0.47), residues: 107 loop : -1.96 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1122 TYR 0.015 0.002 TYR A 325 PHE 0.013 0.001 PHE A 704 TRP 0.014 0.001 TRP A 476 HIS 0.007 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14413) covalent geometry : angle 0.58044 / 0.31 (20059) hydrogen bonds : bond 0.04241 / 4.18 ( 567) hydrogen bonds : angle 4.89542 / 6.19 ( 1540) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.419 Fit side-chains REVERT: A 201 ILE cc_start: -0.1910 (OUTLIER) cc_final: -0.2185 (pp) REVERT: A 241 LEU cc_start: -0.1950 (OUTLIER) cc_final: -0.2584 (mt) REVERT: A 694 MET cc_start: 0.0169 (ppp) cc_final: -0.1941 (mpp) REVERT: A 703 THR cc_start: 0.3401 (OUTLIER) cc_final: 0.2956 (t) REVERT: A 904 GLU cc_start: 0.5191 (tt0) cc_final: 0.3842 (mt-10) REVERT: A 976 ARG cc_start: 0.2174 (ptp-170) cc_final: -0.0182 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3418 (mtp85) cc_final: 0.2400 (mmm160) REVERT: A 1169 MET cc_start: 0.2822 (mtt) cc_final: 0.1909 (mtm) REVERT: C 77 MET cc_start: -0.0645 (mmp) cc_final: -0.1345 (ptm) outliers start: 18 outliers final: 10 residues processed: 83 average time/residue: 0.1210 time to fit residues: 15.1740 Evaluate side-chains 80 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN A1264 HIS ** A1317 ASN ** 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 = 0.5070 r_free = 0.5070 target = 0.265665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.228249 restraints weight = 29277.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.233204 restraints weight = 15657.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.236390 restraints weight = 9874.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.238533 restraints weight = 7104.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.239644 restraints weight = 5651.491| |-----------------------------------------------------------------------------| r_work (final): 0.4905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1354 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14414 Z= 0.113 Angle : 0.565 10.511 20059 Z= 0.300 Chirality : 0.040 0.308 2356 Planarity : 0.004 0.046 2153 Dihedral : 19.412 176.544 3326 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.25 % Allowed : 14.75 % Favored : 84.00 % 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: -1.20 (0.21), residues: 1447 helix: 0.21 (0.20), residues: 680 sheet: -0.87 (0.45), residues: 117 loop : -1.88 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 152 TYR 0.016 0.002 TYR A 325 PHE 0.027 0.002 PHE A 86 TRP 0.015 0.001 TRP A 476 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14413) covalent geometry : angle 0.56539 / 0.30 (20059) hydrogen bonds : bond 0.04101 / 4.04 ( 567) hydrogen bonds : angle 4.79245 / 6.08 ( 1540) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.515 Fit side-chains REVERT: A 201 ILE cc_start: -0.1962 (OUTLIER) cc_final: -0.2223 (pp) REVERT: A 241 LEU cc_start: -0.2138 (OUTLIER) cc_final: -0.2759 (mt) REVERT: A 648 MET cc_start: -0.2755 (tpt) cc_final: -0.3373 (tpt) REVERT: A 694 MET cc_start: 0.0147 (ppp) cc_final: -0.1776 (mpp) REVERT: A 904 GLU cc_start: 0.5479 (tt0) cc_final: 0.4073 (mt-10) REVERT: A 976 ARG cc_start: 0.2368 (ptp-170) cc_final: 0.0128 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3416 (mtp85) cc_final: 0.2369 (mmm160) REVERT: A 1169 MET cc_start: 0.2626 (mtt) cc_final: 0.1747 (mtm) REVERT: C 1 MET cc_start: 0.2025 (ptt) cc_final: -0.0436 (mmt) REVERT: C 77 MET cc_start: -0.0563 (mmp) cc_final: -0.1202 (ptm) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.1284 time to fit residues: 16.1803 Evaluate side-chains 81 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 0.0670 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 723 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.264824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.228107 restraints weight = 29249.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.232863 restraints weight = 15834.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.236021 restraints weight = 10008.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.238111 restraints weight = 7223.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.239276 restraints weight = 5775.935| |-----------------------------------------------------------------------------| r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1454 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14414 Z= 0.126 Angle : 0.599 12.666 20059 Z= 0.315 Chirality : 0.041 0.303 2356 Planarity : 0.004 0.060 2153 Dihedral : 19.379 175.621 3326 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.67 % Allowed : 14.83 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.25 (0.21), residues: 1447 helix: 0.13 (0.20), residues: 680 sheet: -1.09 (0.48), residues: 107 loop : -1.81 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 165 TYR 0.016 0.002 TYR A 362 PHE 0.015 0.002 PHE A 704 TRP 0.019 0.001 TRP A 476 HIS 0.006 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (14413) covalent geometry : angle 0.59895 / 0.32 (20059) hydrogen bonds : bond 0.04315 / 4.24 ( 567) hydrogen bonds : angle 4.81075 / 6.03 ( 1540) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.460 Fit side-chains REVERT: A 201 ILE cc_start: -0.1688 (OUTLIER) cc_final: -0.1964 (pp) REVERT: A 241 LEU cc_start: -0.2185 (OUTLIER) cc_final: -0.2819 (mt) REVERT: A 374 LYS cc_start: 0.6933 (tppt) cc_final: 0.6722 (tptm) REVERT: A 631 MET cc_start: -0.0535 (ptp) cc_final: -0.3051 (tpp) REVERT: A 684 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6640 (ttmt) REVERT: A 694 MET cc_start: 0.0364 (ppp) cc_final: -0.1828 (mpp) REVERT: A 904 GLU cc_start: 0.5476 (tt0) cc_final: 0.4067 (mt-10) REVERT: A 976 ARG cc_start: 0.2231 (ptp-170) cc_final: -0.0122 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3487 (mtp85) cc_final: 0.2414 (mmm160) REVERT: A 1169 MET cc_start: 0.2713 (mtt) cc_final: 0.1794 (mtm) REVERT: C 1 MET cc_start: 0.2142 (ptt) cc_final: -0.0442 (mmt) REVERT: C 77 MET cc_start: -0.0053 (mmp) cc_final: -0.0895 (ptm) outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 0.1220 time to fit residues: 16.2102 Evaluate side-chains 89 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 110 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 9 optimal weight: 20.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 ASN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A1264 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.265217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.228404 restraints weight = 29356.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.233194 restraints weight = 15960.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.236390 restraints weight = 10143.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.238522 restraints weight = 7343.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.239849 restraints weight = 5876.927| |-----------------------------------------------------------------------------| r_work (final): 0.4916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1403 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 14414 Z= 0.109 Angle : 0.565 10.159 20059 Z= 0.300 Chirality : 0.040 0.307 2356 Planarity : 0.004 0.058 2153 Dihedral : 19.336 176.044 3326 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.33 % Allowed : 14.75 % Favored : 83.92 % 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: -1.12 (0.21), residues: 1447 helix: 0.24 (0.20), residues: 680 sheet: -0.86 (0.46), residues: 117 loop : -1.79 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 78 TYR 0.020 0.002 TYR A 362 PHE 0.015 0.001 PHE A 168 TRP 0.015 0.001 TRP A 476 HIS 0.014 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14413) covalent geometry : angle 0.56470 / 0.30 (20059) hydrogen bonds : bond 0.04170 / 4.09 ( 567) hydrogen bonds : angle 4.71897 / 5.95 ( 1540) Misc. bond : bond 0.00025 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.70 seconds wall clock time: 45 minutes 22.55 seconds (2722.55 seconds total)