Starting phenix.real_space_refine on Mon Nov 18 06:07:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6p_41074/11_2024/8t6p_41074.cif" } resolution = 3.15 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5028 atoms to isotropic. 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 110 5.49 5 S 17 5.16 5 C 6707 2.51 5 N 1951 2.21 5 O 2391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8838 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 30, 'TRANS': 1077} Chain breaks: 4 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1887 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 77} Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 8.13, per 1000 atoms: 0.73 Number of scatterers: 11176 At special positions: 0 Unit cell: (85.8196, 120.814, 120.814, 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 17 16.00 P 110 15.00 O 2391 8.00 N 1951 7.00 C 6707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 57.3% alpha, 10.7% beta 34 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.725A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.946A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.659A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.558A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.008A pdb=" N ASN A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.199A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.938A pdb=" N THR A 310 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.560A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.667A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.678A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.214A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.593A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.508A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (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 543 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.527A pdb=" N LYS A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.725A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.245A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.860A pdb=" N ASN A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 668' Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 702 through 712 removed outlier: 4.317A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.060A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.805A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.475A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.756A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.858A pdb=" N PHE A1258 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 4.204A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.314A pdb=" N ILE A1310 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.539A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 5.980A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.814A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499 removed outlier: 5.511A pdb=" N GLU A 505 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 506 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU A 662 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.885A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.885A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.31: 1674 1.31 - 1.49: 5288 1.49 - 1.67: 4616 1.67 - 1.85: 33 1.85 - 2.02: 6 Bond restraints: 11617 Sorted by residual: bond pdb=" CZ ARG A 557 " pdb=" NH1 ARG A 557 " ideal model delta sigma weight residual 1.323 2.024 -0.701 1.40e-02 5.10e+03 2.51e+03 bond pdb=" CZ ARG A 691 " pdb=" NH1 ARG A 691 " ideal model delta sigma weight residual 1.323 2.024 -0.701 1.40e-02 5.10e+03 2.50e+03 bond pdb=" CZ ARG A 586 " pdb=" NH1 ARG A 586 " ideal model delta sigma weight residual 1.323 1.976 -0.653 1.40e-02 5.10e+03 2.17e+03 bond pdb=" CZ ARG A 654 " pdb=" NH2 ARG A 654 " ideal model delta sigma weight residual 1.330 1.898 -0.568 1.30e-02 5.92e+03 1.91e+03 bond pdb=" CD GLN A 194 " pdb=" NE2 GLN A 194 " ideal model delta sigma weight residual 1.328 1.976 -0.648 2.10e-02 2.27e+03 9.52e+02 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.97: 16169 7.97 - 15.93: 26 15.93 - 23.90: 10 23.90 - 31.86: 2 31.86 - 39.83: 1 Bond angle restraints: 16208 Sorted by residual: angle pdb=" NH1 ARG A 557 " pdb=" CZ ARG A 557 " pdb=" NH2 ARG A 557 " ideal model delta sigma weight residual 119.30 159.13 -39.83 1.30e+00 5.92e-01 9.38e+02 angle pdb=" NE ARG A 557 " pdb=" CZ ARG A 557 " pdb=" NH2 ARG A 557 " ideal model delta sigma weight residual 119.20 95.45 23.75 9.00e-01 1.23e+00 6.97e+02 angle pdb=" NE ARG A 494 " pdb=" CZ ARG A 494 " pdb=" NH1 ARG A 494 " ideal model delta sigma weight residual 121.50 146.63 -25.13 1.00e+00 1.00e+00 6.32e+02 angle pdb=" NH1 ARG A 494 " pdb=" CZ ARG A 494 " pdb=" NH2 ARG A 494 " ideal model delta sigma weight residual 119.30 93.19 26.11 1.30e+00 5.92e-01 4.03e+02 angle pdb=" OD1 ASN A 668 " pdb=" CG ASN A 668 " pdb=" ND2 ASN A 668 " ideal model delta sigma weight residual 122.60 102.72 19.88 1.00e+00 1.00e+00 3.95e+02 ... (remaining 16203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.67: 6493 29.67 - 59.35: 470 59.35 - 89.02: 93 89.02 - 118.69: 0 118.69 - 148.36: 1 Dihedral angle restraints: 7057 sinusoidal: 3798 harmonic: 3259 Sorted by residual: dihedral pdb=" C ASP A 284 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" CB ASP A 284 " ideal model delta harmonic sigma weight residual -122.60 -139.46 16.86 0 2.50e+00 1.60e-01 4.55e+01 dihedral pdb=" N ASP A 284 " pdb=" C ASP A 284 " pdb=" CA ASP A 284 " pdb=" CB ASP A 284 " ideal model delta harmonic sigma weight residual 122.80 139.16 -16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" C ASP A 645 " pdb=" N ASP A 645 " pdb=" CA ASP A 645 " pdb=" CB ASP A 645 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 7054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1832 0.129 - 0.259: 57 0.259 - 0.388: 7 0.388 - 0.517: 0 0.517 - 0.647: 1 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA ASP A 284 " pdb=" N ASP A 284 " pdb=" C ASP A 284 " pdb=" CB ASP A 284 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA TYR A1201 " pdb=" N TYR A1201 " pdb=" C TYR A1201 " pdb=" CB TYR A1201 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" P G B 11 " pdb=" OP1 G B 11 " pdb=" OP2 G B 11 " pdb=" O5' G B 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1894 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 62 " -0.220 2.00e-02 2.50e+03 9.27e-02 2.58e+02 pdb=" N9 G B 62 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G B 62 " 0.027 2.00e-02 2.50e+03 pdb=" N7 G B 62 " 0.051 2.00e-02 2.50e+03 pdb=" C5 G B 62 " 0.072 2.00e-02 2.50e+03 pdb=" C6 G B 62 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G B 62 " -0.151 2.00e-02 2.50e+03 pdb=" N1 G B 62 " -0.018 2.00e-02 2.50e+03 pdb=" C2 G B 62 " 0.044 2.00e-02 2.50e+03 pdb=" N2 G B 62 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G B 62 " 0.088 2.00e-02 2.50e+03 pdb=" C4 G B 62 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 20 " 0.127 2.00e-02 2.50e+03 5.55e-02 9.24e+01 pdb=" N9 DG C 20 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG C 20 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DG C 20 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DG C 20 " -0.036 2.00e-02 2.50e+03 pdb=" C6 DG C 20 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG C 20 " 0.070 2.00e-02 2.50e+03 pdb=" N1 DG C 20 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DG C 20 " -0.022 2.00e-02 2.50e+03 pdb=" N2 DG C 20 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DG C 20 " -0.082 2.00e-02 2.50e+03 pdb=" C4 DG C 20 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 464 " -0.103 2.00e-02 2.50e+03 4.99e-02 6.22e+01 pdb=" CG TRP A 464 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 464 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 464 " 0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP A 464 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 464 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 464 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 464 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 464 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 464 " -0.044 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 10 2.22 - 2.89: 3966 2.89 - 3.56: 16096 3.56 - 4.23: 27838 4.23 - 4.90: 43946 Nonbonded interactions: 91856 Sorted by model distance: nonbonded pdb=" O VAL A 452 " pdb=" SD MET A 465 " model vdw 1.556 3.400 nonbonded pdb=" CG1 VAL A 452 " pdb=" CE MET A 465 " model vdw 1.595 3.880 nonbonded pdb=" CE MET A 161 " pdb=" ND1 HIS A 415 " model vdw 1.692 3.540 nonbonded pdb=" O VAL A 452 " pdb=" CG MET A 465 " model vdw 1.949 3.440 nonbonded pdb=" CG GLN A 342 " pdb=" CE MET A 383 " model vdw 1.987 3.860 ... (remaining 91851 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.570 Find NCS groups from input model: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4428 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 : 0.017 0.701 11617 Z= 1.241 Angle : 1.284 39.825 16208 Z= 0.858 Chirality : 0.057 0.647 1897 Planarity : 0.009 0.106 1668 Dihedral : 18.660 148.364 4943 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.64 % Allowed : 17.66 % Favored : 81.70 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1098 helix: -0.94 (0.20), residues: 529 sheet: -0.69 (0.52), residues: 105 loop : -0.64 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.012 TRP A 464 HIS 0.019 0.002 HIS A1297 PHE 0.058 0.005 PHE A 491 TYR 0.095 0.005 TYR A 451 ARG 0.014 0.001 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: -0.0396 (tp) cc_final: -0.1027 (tp) REVERT: A 497 ASN cc_start: -0.3462 (OUTLIER) cc_final: -0.3938 (m110) REVERT: A 501 ASN cc_start: 0.1665 (m-40) cc_final: 0.0361 (m110) REVERT: A 515 TYR cc_start: -0.0495 (t80) cc_final: -0.0820 (t80) REVERT: A 524 LEU cc_start: 0.1022 (mm) cc_final: -0.0663 (mp) REVERT: A 666 LEU cc_start: 0.0547 (tp) cc_final: -0.0604 (tp) REVERT: A 740 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8616 (t) outliers start: 6 outliers final: 1 residues processed: 101 average time/residue: 0.2976 time to fit residues: 41.5090 Evaluate side-chains 74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 1326 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11617 Z= 0.213 Angle : 0.567 6.578 16208 Z= 0.302 Chirality : 0.038 0.208 1897 Planarity : 0.004 0.044 1668 Dihedral : 18.894 153.786 2782 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 15.32 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1098 helix: 0.27 (0.22), residues: 544 sheet: -0.56 (0.50), residues: 117 loop : -0.31 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.016 0.001 PHE A1105 TYR 0.017 0.001 TYR A 594 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.2396 (tm-30) cc_final: 0.2108 (tm-30) REVERT: A 501 ASN cc_start: 0.0511 (m-40) cc_final: -0.1120 (t0) REVERT: A 521 TYR cc_start: -0.0579 (m-10) cc_final: -0.0788 (m-10) REVERT: A 666 LEU cc_start: -0.0047 (tp) cc_final: -0.0334 (tp) REVERT: A 704 PHE cc_start: -0.0410 (m-10) cc_final: -0.0728 (m-10) REVERT: A 723 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6592 (t-170) REVERT: A 1263 LYS cc_start: 0.8830 (pptt) cc_final: 0.8327 (ttmm) REVERT: A 1307 GLU cc_start: 0.7312 (tp30) cc_final: 0.6660 (tp30) outliers start: 21 outliers final: 12 residues processed: 94 average time/residue: 0.2323 time to fit residues: 32.2369 Evaluate side-chains 79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4519 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11617 Z= 0.237 Angle : 0.543 9.919 16208 Z= 0.287 Chirality : 0.038 0.203 1897 Planarity : 0.004 0.040 1668 Dihedral : 18.852 153.088 2777 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.09 % Allowed : 14.89 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1098 helix: 0.71 (0.22), residues: 544 sheet: -0.63 (0.54), residues: 109 loop : -0.34 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.037 0.002 HIS A 723 PHE 0.033 0.002 PHE A 693 TYR 0.016 0.002 TYR A 594 ARG 0.004 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.0244 (t80) cc_final: -0.0147 (t80) REVERT: A 520 VAL cc_start: -0.0408 (OUTLIER) cc_final: -0.0658 (t) REVERT: A 524 LEU cc_start: -0.0689 (mm) cc_final: -0.0900 (mm) REVERT: A 666 LEU cc_start: -0.0225 (tp) cc_final: -0.0440 (tp) REVERT: A 739 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7271 (mp-120) REVERT: A 1258 PHE cc_start: 0.8402 (t80) cc_final: 0.8150 (t80) REVERT: A 1307 GLU cc_start: 0.7422 (tp30) cc_final: 0.6776 (tp30) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.2235 time to fit residues: 31.8029 Evaluate side-chains 87 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11617 Z= 0.160 Angle : 0.498 8.828 16208 Z= 0.262 Chirality : 0.036 0.198 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.751 151.937 2777 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 15.85 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1098 helix: 1.05 (0.23), residues: 549 sheet: -0.53 (0.52), residues: 117 loop : -0.35 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.005 0.001 HIS A 328 PHE 0.013 0.001 PHE A1105 TYR 0.011 0.001 TYR A 450 ARG 0.003 0.000 ARG A 951 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7202 (mp-120) REVERT: A 763 MET cc_start: 0.2928 (tpp) cc_final: 0.2683 (tpt) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 0.2669 time to fit residues: 36.2195 Evaluate side-chains 78 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 563 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4561 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11617 Z= 0.393 Angle : 0.624 8.246 16208 Z= 0.325 Chirality : 0.041 0.213 1897 Planarity : 0.004 0.037 1668 Dihedral : 18.970 154.705 2777 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.68 % Allowed : 14.68 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1098 helix: 0.83 (0.22), residues: 552 sheet: -0.74 (0.51), residues: 117 loop : -0.53 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.007 0.002 HIS A 328 PHE 0.025 0.002 PHE A 98 TYR 0.024 0.002 TYR A 450 ARG 0.006 0.001 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 63 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 LEU cc_start: -0.0426 (OUTLIER) cc_final: -0.0627 (mt) REVERT: A 739 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7504 (mp-120) REVERT: A 1188 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8283 (mtmm) REVERT: A 1307 GLU cc_start: 0.7637 (tp30) cc_final: 0.7089 (tp30) outliers start: 44 outliers final: 27 residues processed: 102 average time/residue: 0.2475 time to fit residues: 36.3358 Evaluate side-chains 86 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 497 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4520 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11617 Z= 0.167 Angle : 0.518 8.242 16208 Z= 0.269 Chirality : 0.036 0.202 1897 Planarity : 0.003 0.037 1668 Dihedral : 18.850 151.818 2777 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.55 % Allowed : 16.81 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1098 helix: 1.10 (0.23), residues: 553 sheet: -0.63 (0.51), residues: 117 loop : -0.38 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.001 PHE A1105 TYR 0.026 0.001 TYR A 594 ARG 0.002 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7233 (mp-120) REVERT: A 1307 GLU cc_start: 0.7517 (tp30) cc_final: 0.7028 (tp30) outliers start: 24 outliers final: 18 residues processed: 89 average time/residue: 0.2812 time to fit residues: 35.2641 Evaluate side-chains 80 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11617 Z= 0.238 Angle : 0.552 9.412 16208 Z= 0.285 Chirality : 0.038 0.205 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.858 152.760 2777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.98 % Allowed : 16.81 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1098 helix: 1.13 (0.23), residues: 552 sheet: -0.66 (0.51), residues: 117 loop : -0.36 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.019 0.002 PHE A1105 TYR 0.019 0.002 TYR A 594 ARG 0.006 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7353 (mp-120) REVERT: A 1307 GLU cc_start: 0.7611 (tp30) cc_final: 0.7091 (tp30) outliers start: 28 outliers final: 24 residues processed: 82 average time/residue: 0.2268 time to fit residues: 27.9565 Evaluate side-chains 81 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4527 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11617 Z= 0.189 Angle : 0.532 9.670 16208 Z= 0.273 Chirality : 0.037 0.203 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.830 152.100 2777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.09 % Allowed : 16.38 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1098 helix: 1.20 (0.23), residues: 551 sheet: -0.64 (0.51), residues: 117 loop : -0.37 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.018 0.001 PHE A1105 TYR 0.014 0.001 TYR A 450 ARG 0.006 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7312 (mp-120) outliers start: 29 outliers final: 23 residues processed: 82 average time/residue: 0.2176 time to fit residues: 26.8874 Evaluate side-chains 79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 64 optimal weight: 0.0010 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4519 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11617 Z= 0.167 Angle : 0.530 11.164 16208 Z= 0.269 Chirality : 0.037 0.201 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.774 151.520 2777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.98 % Allowed : 16.60 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1098 helix: 1.27 (0.23), residues: 551 sheet: -0.56 (0.51), residues: 117 loop : -0.31 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE A1105 TYR 0.013 0.001 TYR A 450 ARG 0.005 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7283 (mp-120) outliers start: 28 outliers final: 23 residues processed: 86 average time/residue: 0.2336 time to fit residues: 29.7449 Evaluate side-chains 85 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.0070 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4541 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11617 Z= 0.251 Angle : 0.572 10.688 16208 Z= 0.292 Chirality : 0.038 0.206 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.857 152.952 2777 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.66 % Allowed : 16.60 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1098 helix: 1.23 (0.23), residues: 550 sheet: -0.73 (0.49), residues: 121 loop : -0.39 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.024 0.001 PHE A1105 TYR 0.022 0.002 TYR A 450 ARG 0.005 0.000 ARG A 967 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 739 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7357 (mp-120) REVERT: A 967 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.8021 (ttm-80) outliers start: 25 outliers final: 22 residues processed: 81 average time/residue: 0.2427 time to fit residues: 28.9174 Evaluate side-chains 83 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.3894 r_free = 0.3894 target = 0.108836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.072083 restraints weight = 26795.442| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.17 r_work: 0.3049 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11617 Z= 0.255 Angle : 0.574 10.106 16208 Z= 0.294 Chirality : 0.039 0.217 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.891 152.904 2777 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.55 % Allowed : 17.13 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1098 helix: 1.20 (0.23), residues: 550 sheet: -0.80 (0.49), residues: 121 loop : -0.42 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.027 0.002 PHE A1105 TYR 0.015 0.001 TYR A 450 ARG 0.007 0.000 ARG A 967 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.50 seconds wall clock time: 45 minutes 4.83 seconds (2704.83 seconds total)