Starting phenix.real_space_refine on Thu Sep 26 23:30:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_8749_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_8749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_8749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_8749_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vzl_8749/09_2024/5vzl_8749_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 7, 'ASP:plan': 7, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 10} 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: 8.94, per 1000 atoms: 0.64 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: 3.80 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.23 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: 6.10 Time building geometry restraints manager: 4.40 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=" C3' A B 47 " pdb=" O3' A B 47 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 2.90e+00 bond pdb=" C GLY A1319 " pdb=" N ALA A1320 " ideal model delta sigma weight residual 1.340 1.243 0.098 5.87e-02 2.90e+02 2.77e+00 bond pdb=" N9 G B 4 " pdb=" C4 G B 4 " ideal model delta sigma weight residual 1.375 1.405 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" CB PHE A 972 " pdb=" CG PHE A 972 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.97e+00 ... (remaining 14408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19515 2.48 - 4.96: 462 4.96 - 7.43: 65 7.43 - 9.91: 14 9.91 - 12.39: 3 Bond angle restraints: 20059 Sorted by residual: angle pdb=" N VAL A1015 " pdb=" CA VAL A1015 " pdb=" C VAL A1015 " ideal model delta sigma weight residual 111.91 106.73 5.18 8.90e-01 1.26e+00 3.38e+01 angle pdb=" C3' A B 47 " pdb=" O3' A B 47 " pdb=" P A B 48 " ideal model delta sigma weight residual 120.20 127.23 -7.03 1.50e+00 4.44e-01 2.20e+01 angle pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" C PHE A 196 " pdb=" N GLU A 197 " pdb=" CA GLU A 197 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C3' A B 86 " pdb=" O3' A B 86 " pdb=" P A B 87 " ideal model delta sigma weight residual 120.20 126.54 -6.34 1.50e+00 4.44e-01 1.79e+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: 1930 0.062 - 0.125: 377 0.125 - 0.187: 39 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=" P A B 48 " pdb=" OP1 A B 48 " pdb=" OP2 A B 48 " pdb=" O5' A B 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.28e+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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.150 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0248 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 14413 Z= 0.366 Angle : 0.958 12.390 20059 Z= 0.508 Chirality : 0.050 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (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 TRP 0.011 0.003 TRP A 464 HIS 0.007 0.002 HIS A1241 PHE 0.020 0.003 PHE A1008 TYR 0.028 0.003 TYR A 973 ARG 0.015 0.001 ARG A 78 *********************** 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 fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: -0.3469 (OUTLIER) cc_final: -0.3722 (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: 0.4064 (ppp) outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.3170 time to fit residues: 55.2417 Evaluate side-chains 82 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 130 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 137 HIS A 194 GLN A 224 ASN A 420 HIS A 501 ASN A 522 ASN A 595 HIS A 709 GLN A 767 ASN A 807 GLN A 863 ASN A1091 GLN A1286 ASN C 2 ASN C 12 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0681 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14413 Z= 0.209 Angle : 0.664 9.536 20059 Z= 0.344 Chirality : 0.040 0.254 2356 Planarity : 0.005 0.066 2153 Dihedral : 19.981 179.828 3330 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.42 % Allowed : 6.33 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1447 helix: -0.96 (0.18), residues: 688 sheet: -1.78 (0.42), residues: 120 loop : -2.21 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.011 0.002 HIS A 328 PHE 0.015 0.002 PHE A 164 TYR 0.020 0.002 TYR A 155 ARG 0.008 0.001 ARG A 340 *********************** 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 112 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.2483 (mmm) cc_final: 0.2102 (mmm) REVERT: A 194 GLN cc_start: -0.2883 (OUTLIER) cc_final: -0.3646 (mm-40) REVERT: A 207 ASP cc_start: 0.5597 (t0) cc_final: 0.4990 (p0) REVERT: A 241 LEU cc_start: -0.2575 (OUTLIER) cc_final: -0.3275 (mp) REVERT: A 822 MET cc_start: -0.4411 (mmm) cc_final: -0.4937 (mtt) REVERT: A 904 GLU cc_start: 0.3886 (tt0) cc_final: 0.3048 (mt-10) REVERT: A 1060 ARG cc_start: 0.3166 (mtp85) cc_final: 0.2330 (mmm160) REVERT: A 1095 VAL cc_start: -0.1488 (t) cc_final: -0.1954 (p) REVERT: A 1148 LYS cc_start: 0.6789 (pttm) cc_final: 0.6550 (pttm) REVERT: A 1328 ASP cc_start: 0.2666 (p0) cc_final: 0.1974 (t70) outliers start: 17 outliers final: 5 residues processed: 110 average time/residue: 0.2822 time to fit residues: 45.4894 Evaluate side-chains 82 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 817 GLN A1091 GLN A1264 HIS A1317 ASN C 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0785 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 14413 Z= 0.161 Angle : 0.566 9.139 20059 Z= 0.293 Chirality : 0.038 0.235 2356 Planarity : 0.004 0.049 2153 Dihedral : 19.620 179.333 3326 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.83 % Allowed : 7.92 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1447 helix: -0.01 (0.19), residues: 701 sheet: -1.30 (0.47), residues: 101 loop : -2.04 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.007 0.001 HIS A1264 PHE 0.011 0.001 PHE C 73 TYR 0.012 0.001 TYR A 656 ARG 0.007 0.001 ARG A 340 *********************** 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 fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4179 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: A 161 MET cc_start: 0.2841 (mmm) cc_final: 0.2362 (mmm) REVERT: A 207 ASP cc_start: 0.5545 (t0) cc_final: 0.4961 (p0) REVERT: A 241 LEU cc_start: -0.3033 (OUTLIER) cc_final: -0.3658 (mp) REVERT: A 383 MET cc_start: 0.3800 (tpp) cc_final: 0.3549 (ttt) REVERT: A 694 MET cc_start: -0.0400 (ppp) cc_final: -0.2381 (mpp) REVERT: A 904 GLU cc_start: 0.4438 (tt0) cc_final: 0.3597 (mt-10) REVERT: A 970 PHE cc_start: 0.1189 (m-80) cc_final: 0.0204 (m-80) REVERT: A 976 ARG cc_start: 0.2046 (ptp-170) cc_final: -0.0172 (ptt180) REVERT: A 1060 ARG cc_start: 0.2955 (mtp85) cc_final: 0.2162 (mmm160) REVERT: A 1089 MET cc_start: -0.0143 (tmm) cc_final: -0.0827 (tmm) REVERT: A 1328 ASP cc_start: 0.2186 (p0) cc_final: 0.1877 (t70) REVERT: C 33 ARG cc_start: 0.3015 (mmt90) cc_final: 0.2691 (mmt90) REVERT: C 80 ILE cc_start: -0.4179 (OUTLIER) cc_final: -0.4937 (pt) outliers start: 22 outliers final: 9 residues processed: 108 average time/residue: 0.2842 time to fit residues: 45.3449 Evaluate side-chains 88 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 151 LEU 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 662 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 80 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 149 optimal weight: 0.0770 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 920 GLN A1241 HIS A1264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1084 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14413 Z= 0.205 Angle : 0.653 9.717 20059 Z= 0.338 Chirality : 0.041 0.219 2356 Planarity : 0.004 0.049 2153 Dihedral : 19.545 174.632 3326 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.92 % Allowed : 9.50 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.21), residues: 1447 helix: 0.07 (0.19), residues: 695 sheet: -0.65 (0.53), residues: 89 loop : -2.18 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 476 HIS 0.012 0.002 HIS A1264 PHE 0.020 0.002 PHE A 626 TYR 0.025 0.002 TYR A 136 ARG 0.011 0.001 ARG A1122 *********************** 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 123 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: -0.2299 (OUTLIER) cc_final: -0.2630 (tp-100) REVERT: A 207 ASP cc_start: 0.5728 (t0) cc_final: 0.5345 (p0) REVERT: A 241 LEU cc_start: -0.2735 (OUTLIER) cc_final: -0.3461 (mp) REVERT: A 609 ASN cc_start: 0.6046 (m110) cc_final: 0.5838 (m110) REVERT: A 694 MET cc_start: 0.0630 (ppp) cc_final: -0.1766 (mpp) REVERT: A 904 GLU cc_start: 0.4877 (tt0) cc_final: 0.3894 (mt-10) REVERT: A 970 PHE cc_start: 0.1904 (m-80) cc_final: 0.0539 (m-80) REVERT: A 976 ARG cc_start: 0.1828 (ptp-170) cc_final: -0.0572 (ptt180) REVERT: A 1018 VAL cc_start: 0.4462 (OUTLIER) cc_final: 0.4238 (m) REVERT: A 1060 ARG cc_start: 0.3294 (mtp85) cc_final: 0.2438 (mmm160) REVERT: A 1333 ARG cc_start: 0.1522 (OUTLIER) cc_final: -0.0190 (ptm160) outliers start: 35 outliers final: 17 residues processed: 115 average time/residue: 0.2846 time to fit residues: 47.4295 Evaluate side-chains 95 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 662 LEU 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 A residue 1213 MET 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 28 THR Chi-restraints excluded: chain C residue 34 VAL 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 85 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS A1286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1038 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14413 Z= 0.134 Angle : 0.543 9.309 20059 Z= 0.279 Chirality : 0.038 0.200 2356 Planarity : 0.003 0.045 2153 Dihedral : 19.343 175.742 3326 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.00 % Allowed : 11.00 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1447 helix: 0.60 (0.20), residues: 683 sheet: -0.35 (0.59), residues: 79 loop : -1.87 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.016 0.001 HIS A1264 PHE 0.013 0.001 PHE A 196 TYR 0.012 0.001 TYR A 325 ARG 0.005 0.000 ARG A1122 *********************** 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 101 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.5739 (t0) cc_final: 0.5454 (p0) REVERT: A 241 LEU cc_start: -0.3004 (OUTLIER) cc_final: -0.3665 (mp) REVERT: A 346 LYS cc_start: 0.1432 (OUTLIER) cc_final: 0.0990 (pttm) REVERT: A 609 ASN cc_start: 0.6203 (m110) cc_final: 0.5988 (m110) REVERT: A 694 MET cc_start: 0.0725 (ppp) cc_final: -0.1492 (mpp) REVERT: A 904 GLU cc_start: 0.5296 (tt0) cc_final: 0.4343 (mt-10) REVERT: A 970 PHE cc_start: 0.1657 (m-80) cc_final: 0.0580 (m-80) REVERT: A 976 ARG cc_start: 0.2084 (ptp-170) cc_final: -0.0680 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3321 (mtp85) cc_final: 0.2403 (mmm160) REVERT: A 1333 ARG cc_start: 0.1002 (OUTLIER) cc_final: -0.0876 (ptm160) REVERT: C 33 ARG cc_start: 0.4637 (mmt90) cc_final: 0.4034 (mmt180) outliers start: 24 outliers final: 10 residues processed: 97 average time/residue: 0.2596 time to fit residues: 37.8313 Evaluate side-chains 88 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1131 TYR Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1333 ARG Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 80 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 78 optimal weight: 0.0020 chunk 144 optimal weight: 5.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A1264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1045 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14413 Z= 0.125 Angle : 0.537 12.637 20059 Z= 0.270 Chirality : 0.037 0.204 2356 Planarity : 0.003 0.047 2153 Dihedral : 19.132 176.055 3326 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.67 % Allowed : 12.33 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1447 helix: 0.88 (0.20), residues: 681 sheet: -0.35 (0.55), residues: 89 loop : -1.68 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.016 0.001 HIS A1264 PHE 0.016 0.001 PHE A 119 TYR 0.013 0.001 TYR A 325 ARG 0.004 0.000 ARG A1122 *********************** 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 100 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: -0.2144 (OUTLIER) cc_final: -0.3199 (mm-40) REVERT: A 207 ASP cc_start: 0.5845 (t0) cc_final: 0.5565 (p0) REVERT: A 241 LEU cc_start: -0.2958 (OUTLIER) cc_final: -0.3656 (mp) REVERT: A 346 LYS cc_start: 0.1502 (OUTLIER) cc_final: 0.1056 (pttm) REVERT: A 648 MET cc_start: -0.4161 (tpt) cc_final: -0.4384 (tpt) REVERT: A 694 MET cc_start: 0.0295 (ppp) cc_final: -0.1894 (mpp) REVERT: A 904 GLU cc_start: 0.5117 (tt0) cc_final: 0.4171 (mt-10) REVERT: A 939 MET cc_start: -0.0722 (ptt) cc_final: -0.1939 (ptp) REVERT: A 970 PHE cc_start: 0.1688 (m-80) cc_final: 0.0740 (m-80) REVERT: A 976 ARG cc_start: 0.2038 (ptp-170) cc_final: -0.0764 (ptt-90) REVERT: A 1060 ARG cc_start: 0.3011 (mtp85) cc_final: 0.1970 (tpt90) REVERT: A 1333 ARG cc_start: 0.1164 (OUTLIER) cc_final: -0.0855 (ptm160) REVERT: C 33 ARG cc_start: 0.4813 (mmt90) cc_final: 0.4097 (mmt180) outliers start: 20 outliers final: 12 residues processed: 99 average time/residue: 0.2649 time to fit residues: 39.6792 Evaluate side-chains 91 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 1015 VAL 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 28 THR Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 0.0040 chunk 93 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 224 ASN A 255 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 415 HIS A 723 HIS ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1310 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14413 Z= 0.197 Angle : 0.655 11.079 20059 Z= 0.332 Chirality : 0.041 0.224 2356 Planarity : 0.004 0.046 2153 Dihedral : 19.364 170.814 3326 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.33 % Allowed : 11.92 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1447 helix: 0.38 (0.20), residues: 674 sheet: -0.15 (0.58), residues: 77 loop : -1.74 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 476 HIS 0.023 0.002 HIS A1264 PHE 0.024 0.002 PHE A 119 TYR 0.020 0.002 TYR A 359 ARG 0.017 0.001 ARG A 557 *********************** 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 110 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: -0.2980 (OUTLIER) cc_final: -0.3640 (mt) REVERT: A 401 LYS cc_start: 0.5137 (mttt) cc_final: 0.4728 (mmtt) REVERT: A 648 MET cc_start: -0.3775 (tpt) cc_final: -0.3981 (tpt) REVERT: A 694 MET cc_start: 0.0308 (ppp) cc_final: -0.2294 (mpp) REVERT: A 939 MET cc_start: -0.0525 (ptt) cc_final: -0.1700 (ptp) REVERT: A 970 PHE cc_start: 0.2637 (m-80) cc_final: 0.2251 (m-80) REVERT: A 976 ARG cc_start: 0.2600 (ptp-170) cc_final: -0.0461 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1013 (mt-10) cc_final: 0.0746 (tm-30) REVERT: A 1060 ARG cc_start: 0.2467 (mtp85) cc_final: 0.2100 (mmm160) REVERT: A 1264 HIS cc_start: 0.2818 (t-90) cc_final: 0.2416 (p90) REVERT: A 1333 ARG cc_start: 0.1763 (OUTLIER) cc_final: 0.0173 (ptm160) REVERT: C 33 ARG cc_start: 0.4470 (mmt90) cc_final: 0.3933 (mmt180) outliers start: 28 outliers final: 15 residues processed: 102 average time/residue: 0.2884 time to fit residues: 43.5139 Evaluate side-chains 92 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 642 LEU 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 1213 MET Chi-restraints excluded: chain A residue 1331 ILE 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 28 THR Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 101 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 255 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1291 moved from start: 0.8326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 14413 Z= 0.161 Angle : 0.596 9.687 20059 Z= 0.306 Chirality : 0.039 0.248 2356 Planarity : 0.004 0.045 2153 Dihedral : 19.269 173.735 3326 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.25 % Allowed : 12.33 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1447 helix: 0.41 (0.20), residues: 685 sheet: -0.70 (0.49), residues: 98 loop : -1.82 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.009 0.001 HIS A 412 PHE 0.024 0.002 PHE A 119 TYR 0.013 0.002 TYR A 656 ARG 0.004 0.001 ARG A 340 *********************** 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 108 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: -0.0866 (mmt) cc_final: -0.1091 (mmt) REVERT: A 194 GLN cc_start: -0.1460 (OUTLIER) cc_final: -0.2726 (mm-40) REVERT: A 241 LEU cc_start: -0.2997 (OUTLIER) cc_final: -0.3686 (mt) REVERT: A 346 LYS cc_start: 0.2373 (OUTLIER) cc_final: 0.1821 (pttm) REVERT: A 401 LYS cc_start: 0.5384 (mttt) cc_final: 0.4948 (mmtt) REVERT: A 694 MET cc_start: 0.0257 (ppp) cc_final: -0.2272 (mpp) REVERT: A 904 GLU cc_start: 0.5087 (tt0) cc_final: 0.4142 (mt-10) REVERT: A 939 MET cc_start: -0.0511 (ptt) cc_final: -0.1351 (ptp) REVERT: A 970 PHE cc_start: 0.2776 (m-80) cc_final: 0.2411 (m-80) REVERT: A 976 ARG cc_start: 0.2729 (ptp-170) cc_final: -0.0260 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1555 (mt-10) cc_final: 0.1138 (tm-30) REVERT: A 1060 ARG cc_start: 0.2246 (mtp85) cc_final: 0.1856 (tpt90) REVERT: A 1264 HIS cc_start: 0.2898 (t-90) cc_final: 0.2288 (p-80) REVERT: A 1333 ARG cc_start: 0.1558 (OUTLIER) cc_final: -0.0043 (ptm160) REVERT: C 33 ARG cc_start: 0.4372 (mmt90) cc_final: 0.3888 (mmt180) outliers start: 27 outliers final: 14 residues processed: 103 average time/residue: 0.2767 time to fit residues: 42.3672 Evaluate side-chains 94 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 826 GLN 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 1213 MET 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 28 THR Chi-restraints excluded: chain C residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 255 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 863 ASN ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1272 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 14413 Z= 0.145 Angle : 0.572 10.510 20059 Z= 0.293 Chirality : 0.038 0.230 2356 Planarity : 0.003 0.045 2153 Dihedral : 19.155 175.131 3326 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.58 % Allowed : 12.67 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.21), residues: 1447 helix: 0.57 (0.20), residues: 684 sheet: -0.53 (0.52), residues: 96 loop : -1.77 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.020 0.001 PHE A 119 TYR 0.015 0.001 TYR A 325 ARG 0.005 0.000 ARG A1333 *********************** 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 95 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 151 LEU cc_start: -0.3681 (OUTLIER) cc_final: -0.3992 (tp) REVERT: A 194 GLN cc_start: -0.1587 (OUTLIER) cc_final: -0.2600 (mm110) REVERT: A 241 LEU cc_start: -0.2989 (OUTLIER) cc_final: -0.3719 (mt) REVERT: A 346 LYS cc_start: 0.2523 (OUTLIER) cc_final: 0.1937 (pttm) REVERT: A 401 LYS cc_start: 0.5574 (mttt) cc_final: 0.5102 (mmtt) REVERT: A 694 MET cc_start: 0.0141 (ppp) cc_final: -0.2511 (mpp) REVERT: A 904 GLU cc_start: 0.5095 (tt0) cc_final: 0.4155 (mt-10) REVERT: A 939 MET cc_start: -0.0472 (ptt) cc_final: -0.1327 (ptp) REVERT: A 970 PHE cc_start: 0.2870 (m-80) cc_final: 0.2561 (m-80) REVERT: A 976 ARG cc_start: 0.2601 (ptp-170) cc_final: -0.0353 (ptt-90) REVERT: A 977 GLU cc_start: 0.3817 (tp30) cc_final: 0.3120 (pm20) REVERT: A 1056 GLU cc_start: 0.1583 (mt-10) cc_final: 0.1159 (tm-30) REVERT: A 1060 ARG cc_start: 0.2212 (mtp85) cc_final: 0.1695 (tpt90) REVERT: A 1264 HIS cc_start: 0.2401 (t-90) cc_final: 0.1982 (p90) REVERT: C 1 MET cc_start: 0.2138 (ptt) cc_final: -0.0709 (mmt) REVERT: C 33 ARG cc_start: 0.4556 (mmt90) cc_final: 0.3878 (mmt180) REVERT: C 71 GLU cc_start: -0.2018 (OUTLIER) cc_final: -0.2783 (pm20) outliers start: 19 outliers final: 11 residues processed: 91 average time/residue: 0.2623 time to fit residues: 36.1422 Evaluate side-chains 91 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 398 LEU 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 1213 MET Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 255 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1379 moved from start: 0.9167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14413 Z= 0.171 Angle : 0.620 10.736 20059 Z= 0.317 Chirality : 0.039 0.210 2356 Planarity : 0.004 0.059 2153 Dihedral : 19.181 174.638 3326 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.75 % Allowed : 12.50 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1447 helix: 0.48 (0.20), residues: 682 sheet: -0.76 (0.50), residues: 103 loop : -1.82 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.030 0.002 PHE A 119 TYR 0.013 0.002 TYR A1265 ARG 0.014 0.001 ARG A 557 ********************** 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 99 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.355 Fit side-chains REVERT: A 194 GLN cc_start: -0.1824 (OUTLIER) cc_final: -0.2746 (mm-40) REVERT: A 241 LEU cc_start: -0.2973 (OUTLIER) cc_final: -0.3755 (mt) REVERT: A 346 LYS cc_start: 0.3025 (OUTLIER) cc_final: 0.2402 (pttm) REVERT: A 401 LYS cc_start: 0.5806 (mttt) cc_final: 0.5047 (mmtt) REVERT: A 648 MET cc_start: -0.3372 (tpt) cc_final: -0.3749 (tpt) REVERT: A 939 MET cc_start: -0.0257 (ptt) cc_final: -0.1303 (ptp) REVERT: A 970 PHE cc_start: 0.2949 (m-80) cc_final: 0.2467 (m-80) REVERT: A 976 ARG cc_start: 0.2690 (ptp-170) cc_final: -0.0080 (ptt-90) REVERT: A 1056 GLU cc_start: 0.1753 (mt-10) cc_final: 0.1480 (tp30) REVERT: A 1060 ARG cc_start: 0.2391 (mtp85) cc_final: 0.1825 (tpt90) REVERT: C 1 MET cc_start: 0.1960 (ptt) cc_final: -0.0789 (mmt) REVERT: C 33 ARG cc_start: 0.4315 (mmt90) cc_final: 0.3692 (mmt180) REVERT: C 37 ASP cc_start: 0.7632 (t0) cc_final: 0.6258 (m-30) REVERT: C 71 GLU cc_start: -0.2440 (OUTLIER) cc_final: -0.3163 (pm20) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.2834 time to fit residues: 39.6671 Evaluate side-chains 96 residues out of total 1307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 826 GLN 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 1213 MET Chi-restraints excluded: chain A residue 1326 TYR 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 28 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 113 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0000 chunk 108 optimal weight: 0.5980 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** A1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.264097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.229378 restraints weight = 31700.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.234174 restraints weight = 17658.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.237360 restraints weight = 11343.446| |-----------------------------------------------------------------------------| r_work (final): 0.4852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1491 moved from start: 0.9287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14413 Z= 0.133 Angle : 0.557 7.569 20059 Z= 0.282 Chirality : 0.037 0.201 2356 Planarity : 0.003 0.043 2153 Dihedral : 19.038 174.569 3326 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.33 % Allowed : 12.92 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1447 helix: 0.75 (0.20), residues: 683 sheet: -0.48 (0.54), residues: 96 loop : -1.68 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.014 0.001 HIS A1241 PHE 0.027 0.001 PHE A 119 TYR 0.016 0.001 TYR A 325 ARG 0.005 0.000 ARG A 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.67 seconds wall clock time: 46 minutes 45.67 seconds (2805.67 seconds total)