Starting phenix.real_space_refine on Sat Mar 16 06:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z4j_14499/03_2024/7z4j_14499.pdb" } resolution = 2.99 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= 0.002 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 138 5.49 5 Mg 4 5.21 5 S 22 5.16 5 C 8344 2.51 5 N 2443 2.21 5 O 2997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13948 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2081 Classifications: {'DNA': 1, 'RNA': 97} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 85} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G%5*END:plan2': 1, ' G%5*END:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "C" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 324 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG%5*END:plan2': 1, ' DG%5*END:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 269 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 10999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10999 Classifications: {'peptide': 1345} Link IDs: {'PTRANS': 35, 'TRANS': 1309} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.44, per 1000 atoms: 0.61 Number of scatterers: 13948 At special positions: 0 Unit cell: (85.15, 119.6, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 138 15.00 Mg 4 11.99 O 2997 8.00 N 2443 7.00 C 8344 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 - 3.50 Amino acid : False - 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: 6.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 10 sheets defined 55.7% alpha, 9.7% beta 50 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'B' and resid 59 through 94 removed outlier: 4.818A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.706A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.835A pdb=" N LEU B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.600A pdb=" N PHE B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 307 Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 382 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.810A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.157A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.545A pdb=" N VAL B 481 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 512 through 526 removed outlier: 3.997A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.622A pdb=" N LEU B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 668 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 703 through 712 Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 731 through 751 removed outlier: 4.385A pdb=" N LYS B 735 " --> pdb=" O PRO B 731 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 776 Processing helix chain 'B' and resid 779 through 792 removed outlier: 3.550A pdb=" N ARG B 783 " --> pdb=" O GLU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 804 through 807 Processing helix chain 'B' and resid 808 through 817 Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 860 through 867 Processing helix chain 'B' and resid 872 through 889 removed outlier: 5.303A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR B 882 " --> pdb=" O LYS B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 Processing helix chain 'B' and resid 902 through 904 No H-bonds generated for 'chain 'B' and resid 902 through 904' Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.417A pdb=" N GLY B 915 " --> pdb=" O ASP B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 940 removed outlier: 4.012A pdb=" N LEU B 921 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 970 Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.458A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1030 through 1043 removed outlier: 4.309A pdb=" N MET B1043 " --> pdb=" O TYR B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1047 Processing helix chain 'B' and resid 1078 through 1088 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1186 Processing helix chain 'B' and resid 1229 through 1240 Processing helix chain 'B' and resid 1248 through 1262 Processing helix chain 'B' and resid 1263 through 1280 removed outlier: 4.326A pdb=" N ASP B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1314 through 1317 removed outlier: 3.575A pdb=" N ASN B1317 " --> pdb=" O THR B1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1314 through 1317' Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 959 removed outlier: 4.632A pdb=" N ILE B 11 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 46 removed outlier: 9.929A pdb=" N GLU B1357 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS B 33 " --> pdb=" O GLU B1357 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG B1359 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 35 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP B1361 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.621A pdb=" N LEU B 662 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'B' and resid 836 through 840 Processing sheet with id=AA6, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 3.881A pdb=" N TRP B1074 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1163 removed outlier: 7.224A pdb=" N ILE B1166 " --> pdb=" O ALA B1140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1156 through 1163 Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 536 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 7.57 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2474 1.33 - 1.45: 4187 1.45 - 1.57: 7502 1.57 - 1.69: 276 1.69 - 1.81: 42 Bond restraints: 14481 Sorted by residual: bond pdb=" C ARG B1333 " pdb=" O ARG B1333 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.21e-02 6.83e+03 2.56e+00 bond pdb=" O5' DC C 17 " pdb=" C5' DC C 17 " ideal model delta sigma weight residual 1.423 1.375 0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " ideal model delta sigma weight residual 1.523 1.494 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" O5' DC C 10 " pdb=" C5' DC C 10 " ideal model delta sigma weight residual 1.423 1.382 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" C4' DA C 8 " pdb=" C3' DA C 8 " ideal model delta sigma weight residual 1.523 1.498 0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 14476 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 915 106.02 - 113.01: 8025 113.01 - 119.99: 5067 119.99 - 126.98: 5719 126.98 - 133.97: 420 Bond angle restraints: 20146 Sorted by residual: angle pdb=" CA LEU B1312 " pdb=" CB LEU B1312 " pdb=" CG LEU B1312 " ideal model delta sigma weight residual 116.30 124.05 -7.75 3.50e+00 8.16e-02 4.90e+00 angle pdb=" C2' U A 59 " pdb=" C1' U A 59 " pdb=" N1 U A 59 " ideal model delta sigma weight residual 114.00 110.68 3.32 1.50e+00 4.44e-01 4.89e+00 angle pdb=" C2' U A 23 " pdb=" C1' U A 23 " pdb=" N1 U A 23 " ideal model delta sigma weight residual 112.00 114.97 -2.97 1.50e+00 4.44e-01 3.91e+00 angle pdb=" C2' G A 54 " pdb=" C1' G A 54 " pdb=" N9 G A 54 " ideal model delta sigma weight residual 112.00 114.81 -2.81 1.50e+00 4.44e-01 3.50e+00 angle pdb=" NE ARG B1333 " pdb=" CZ ARG B1333 " pdb=" NH1 ARG B1333 " ideal model delta sigma weight residual 121.50 119.73 1.77 1.00e+00 1.00e+00 3.12e+00 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.77: 7965 19.77 - 39.53: 520 39.53 - 59.30: 228 59.30 - 79.07: 79 79.07 - 98.83: 6 Dihedral angle restraints: 8798 sinusoidal: 4846 harmonic: 3952 Sorted by residual: dihedral pdb=" O4' G A 82 " pdb=" C1' G A 82 " pdb=" N9 G A 82 " pdb=" C4 G A 82 " ideal model delta sinusoidal sigma weight residual 70.00 15.72 54.28 1 2.00e+01 2.50e-03 9.99e+00 dihedral pdb=" N ARG B 653 " pdb=" CA ARG B 653 " pdb=" CB ARG B 653 " pdb=" CG ARG B 653 " ideal model delta sinusoidal sigma weight residual -60.00 -119.38 59.38 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" O5' C A 91 " pdb=" C5' C A 91 " pdb=" C4' C A 91 " pdb=" C3' C A 91 " ideal model delta sinusoidal sigma weight residual -65.00 -123.58 58.58 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 8795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1409 0.028 - 0.056: 604 0.056 - 0.083: 203 0.083 - 0.111: 66 0.111 - 0.139: 23 Chirality restraints: 2305 Sorted by residual: chirality pdb=" C1' A A 51 " pdb=" O4' A A 51 " pdb=" C2' A A 51 " pdb=" N9 A A 51 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" C3' DC c -1 " pdb=" C4' DC c -1 " pdb=" O3' DC c -1 " pdb=" C2' DC c -1 " both_signs ideal model delta sigma weight residual False -2.66 -2.52 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL B 870 " pdb=" N VAL B 870 " pdb=" C VAL B 870 " pdb=" CB VAL B 870 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 2302 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 59 " 0.019 2.00e-02 2.50e+03 1.16e-02 3.04e+00 pdb=" N1 U A 59 " -0.029 2.00e-02 2.50e+03 pdb=" C2 U A 59 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U A 59 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U A 59 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U A 59 " 0.003 2.00e-02 2.50e+03 pdb=" C5 U A 59 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 23 " -0.020 2.00e-02 2.50e+03 1.12e-02 2.83e+00 pdb=" N1 U A 23 " 0.026 2.00e-02 2.50e+03 pdb=" C2 U A 23 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A 23 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U A 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U A 23 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 23 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U A 23 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U A 23 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 54 " 0.022 2.00e-02 2.50e+03 9.66e-03 2.80e+00 pdb=" N9 G A 54 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G A 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 54 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 54 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 54 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 54 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 54 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G A 54 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 54 " -0.002 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 98 2.47 - 3.08: 9436 3.08 - 3.68: 22427 3.68 - 4.29: 33800 4.29 - 4.90: 53227 Nonbonded interactions: 118988 Sorted by model distance: nonbonded pdb=" OP2 DT C 4 " pdb="MG MG B1403 " model vdw 1.860 2.170 nonbonded pdb=" OP1 DT D -3 " pdb="MG MG B1401 " model vdw 1.889 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 303 " model vdw 1.907 2.170 nonbonded pdb="MG MG B1403 " pdb=" O HOH B1501 " model vdw 1.932 2.170 nonbonded pdb="MG MG A 201 " pdb=" O HOH A 306 " model vdw 1.937 2.170 ... (remaining 118983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.060 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 47.630 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.005 0.048 14481 Z= 0.268 Angle : 0.477 7.748 20146 Z= 0.259 Chirality : 0.037 0.139 2305 Planarity : 0.003 0.026 2070 Dihedral : 16.164 98.833 6242 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.15 % Allowed : 6.21 % Favored : 91.64 % 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: 0.96 (0.23), residues: 1339 helix: 1.51 (0.20), residues: 691 sheet: -0.59 (0.46), residues: 130 loop : -0.10 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.010 0.001 PHE B1204 TYR 0.009 0.001 TYR B 155 ARG 0.003 0.000 ARG B 925 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 LEU cc_start: 0.9174 (mt) cc_final: 0.8937 (mp) REVERT: B 248 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5375 (tm) REVERT: B 879 MET cc_start: 0.8413 (mmm) cc_final: 0.7928 (mmm) REVERT: B 1078 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.7776 (ptm-80) outliers start: 26 outliers final: 4 residues processed: 101 average time/residue: 1.5233 time to fit residues: 167.5914 Evaluate side-chains 36 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1033 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 588 ASN B 650 GLN B 668 ASN B 695 GLN B 805 GLN B 826 GLN B 844 GLN B 885 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14481 Z= 0.146 Angle : 0.453 6.386 20146 Z= 0.242 Chirality : 0.035 0.133 2305 Planarity : 0.003 0.029 2070 Dihedral : 17.910 96.560 3392 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.08 % Allowed : 10.51 % Favored : 88.41 % 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: 1.23 (0.23), residues: 1339 helix: 1.81 (0.20), residues: 696 sheet: -0.73 (0.47), residues: 119 loop : -0.08 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.023 0.001 PHE B 290 TYR 0.009 0.001 TYR B 155 ARG 0.005 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 1.485 Fit side-chains REVERT: B 220 ARG cc_start: 0.8824 (mmm-85) cc_final: 0.8539 (tpp-160) REVERT: B 248 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5395 (tm) REVERT: B 534 MET cc_start: 0.8287 (mtp) cc_final: 0.7937 (mtm) REVERT: B 879 MET cc_start: 0.8339 (mmm) cc_final: 0.7904 (mmm) REVERT: B 1078 ARG cc_start: 0.8411 (ptp-110) cc_final: 0.7850 (ptm-80) REVERT: B 1189 GLU cc_start: 0.8194 (mp0) cc_final: 0.7913 (pm20) outliers start: 13 outliers final: 4 residues processed: 48 average time/residue: 1.3771 time to fit residues: 73.6083 Evaluate side-chains 36 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 930 HIS B1262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14481 Z= 0.204 Angle : 0.447 6.405 20146 Z= 0.239 Chirality : 0.035 0.132 2305 Planarity : 0.003 0.034 2070 Dihedral : 17.849 99.496 3389 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 11.01 % Favored : 87.50 % 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: 1.24 (0.23), residues: 1339 helix: 1.83 (0.20), residues: 694 sheet: -0.71 (0.47), residues: 119 loop : -0.09 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.031 0.001 PHE B 290 TYR 0.022 0.001 TYR B1013 ARG 0.005 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 31 time to evaluate : 1.585 Fit side-chains REVERT: B 216 LEU cc_start: 0.9009 (mp) cc_final: 0.8417 (pp) REVERT: B 248 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5388 (tm) REVERT: B 534 MET cc_start: 0.8274 (mtp) cc_final: 0.7893 (mtm) REVERT: B 879 MET cc_start: 0.8472 (mmm) cc_final: 0.7967 (mmm) REVERT: B 1078 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.7861 (ptm-80) outliers start: 18 outliers final: 9 residues processed: 48 average time/residue: 1.3186 time to fit residues: 71.0463 Evaluate side-chains 40 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 0.0770 chunk 69 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14481 Z= 0.204 Angle : 0.441 6.448 20146 Z= 0.237 Chirality : 0.035 0.134 2305 Planarity : 0.003 0.034 2070 Dihedral : 17.832 99.429 3389 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.82 % Allowed : 11.09 % Favored : 87.09 % 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: 1.27 (0.23), residues: 1339 helix: 1.86 (0.20), residues: 696 sheet: -0.76 (0.47), residues: 119 loop : -0.07 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.009 0.001 PHE B1204 TYR 0.023 0.001 TYR B1013 ARG 0.007 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 31 time to evaluate : 1.506 Fit side-chains REVERT: B 248 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5473 (tm) REVERT: B 534 MET cc_start: 0.8270 (mtp) cc_final: 0.7845 (mtm) REVERT: B 879 MET cc_start: 0.8502 (mmm) cc_final: 0.7952 (mmm) REVERT: B 1242 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7490 (m-80) outliers start: 22 outliers final: 12 residues processed: 52 average time/residue: 1.2144 time to fit residues: 71.3890 Evaluate side-chains 43 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14481 Z= 0.153 Angle : 0.427 8.488 20146 Z= 0.227 Chirality : 0.034 0.150 2305 Planarity : 0.003 0.034 2070 Dihedral : 17.790 99.602 3389 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.66 % Allowed : 11.92 % Favored : 86.42 % 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: 1.34 (0.23), residues: 1339 helix: 1.92 (0.20), residues: 696 sheet: -0.65 (0.47), residues: 117 loop : -0.07 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.008 0.001 PHE B1045 TYR 0.025 0.001 TYR B1013 ARG 0.006 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 30 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5453 (tm) REVERT: B 534 MET cc_start: 0.8139 (mtp) cc_final: 0.7736 (mtm) REVERT: B 879 MET cc_start: 0.8527 (mmm) cc_final: 0.7955 (mmm) REVERT: B 1242 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7419 (m-80) outliers start: 20 outliers final: 12 residues processed: 49 average time/residue: 1.0488 time to fit residues: 58.6247 Evaluate side-chains 43 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 535 ARG Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1299 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14481 Z= 0.310 Angle : 0.489 7.952 20146 Z= 0.259 Chirality : 0.037 0.134 2305 Planarity : 0.003 0.037 2070 Dihedral : 17.856 100.017 3389 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 12.00 % Favored : 85.76 % 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: 1.23 (0.23), residues: 1339 helix: 1.81 (0.20), residues: 701 sheet: -0.70 (0.48), residues: 115 loop : -0.11 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE B1204 TYR 0.026 0.001 TYR B1013 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 30 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: B 248 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5406 (tm) REVERT: B 534 MET cc_start: 0.8150 (mtp) cc_final: 0.7813 (mtm) REVERT: B 535 ARG cc_start: 0.7573 (tpm170) cc_final: 0.7363 (OUTLIER) REVERT: B 1042 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8635 (tp) REVERT: B 1242 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7621 (m-80) outliers start: 27 outliers final: 15 residues processed: 53 average time/residue: 1.1756 time to fit residues: 70.6429 Evaluate side-chains 46 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 29 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1299 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 GLN ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14481 Z= 0.157 Angle : 0.428 8.217 20146 Z= 0.228 Chirality : 0.034 0.137 2305 Planarity : 0.002 0.035 2070 Dihedral : 17.744 99.471 3389 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.66 % Allowed : 12.75 % Favored : 85.60 % 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: 1.34 (0.23), residues: 1339 helix: 1.93 (0.20), residues: 693 sheet: -0.61 (0.48), residues: 115 loop : -0.08 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.007 0.001 PHE B1045 TYR 0.024 0.001 TYR B1013 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 30 time to evaluate : 1.537 Fit side-chains REVERT: B 534 MET cc_start: 0.8134 (mtp) cc_final: 0.7744 (mtm) REVERT: B 535 ARG cc_start: 0.7577 (tpm170) cc_final: 0.7365 (OUTLIER) REVERT: B 1242 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7491 (m-80) outliers start: 20 outliers final: 13 residues processed: 47 average time/residue: 1.0861 time to fit residues: 59.0443 Evaluate side-chains 42 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1146 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14481 Z= 0.162 Angle : 0.424 8.706 20146 Z= 0.226 Chirality : 0.034 0.142 2305 Planarity : 0.002 0.034 2070 Dihedral : 17.673 99.257 3387 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.57 % Allowed : 12.83 % Favored : 85.60 % 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: 1.37 (0.23), residues: 1339 helix: 1.97 (0.20), residues: 692 sheet: -0.59 (0.48), residues: 115 loop : -0.09 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.008 0.001 PHE B1204 TYR 0.028 0.001 TYR B1013 ARG 0.004 0.000 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 29 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: B 534 MET cc_start: 0.8178 (mtp) cc_final: 0.7801 (mtm) REVERT: B 1242 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7388 (m-80) outliers start: 19 outliers final: 13 residues processed: 46 average time/residue: 1.1356 time to fit residues: 59.6847 Evaluate side-chains 44 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1240 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Chi-restraints excluded: chain B residue 1299 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14481 Z= 0.145 Angle : 0.420 8.986 20146 Z= 0.224 Chirality : 0.034 0.134 2305 Planarity : 0.002 0.034 2070 Dihedral : 17.632 98.795 3387 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.57 % Allowed : 12.83 % Favored : 85.60 % 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: 1.44 (0.23), residues: 1339 helix: 2.02 (0.20), residues: 693 sheet: -0.56 (0.48), residues: 115 loop : -0.05 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.007 0.001 PHE B1045 TYR 0.025 0.001 TYR B1013 ARG 0.003 0.000 ARG B 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: B 534 MET cc_start: 0.8098 (mtp) cc_final: 0.7783 (mtm) REVERT: B 1058 ARG cc_start: 0.4301 (OUTLIER) cc_final: 0.3996 (mpt-90) REVERT: B 1242 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7346 (m-80) outliers start: 19 outliers final: 12 residues processed: 49 average time/residue: 1.3744 time to fit residues: 75.0527 Evaluate side-chains 43 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1058 ARG Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1221 GLN ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14481 Z= 0.245 Angle : 0.462 9.031 20146 Z= 0.244 Chirality : 0.036 0.134 2305 Planarity : 0.003 0.037 2070 Dihedral : 17.683 98.758 3387 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.49 % Allowed : 13.16 % Favored : 85.35 % 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: 1.37 (0.24), residues: 1339 helix: 1.95 (0.20), residues: 692 sheet: -0.63 (0.48), residues: 115 loop : -0.06 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 476 HIS 0.004 0.001 HIS B 328 PHE 0.011 0.001 PHE B1204 TYR 0.026 0.001 TYR B1013 ARG 0.007 0.000 ARG B 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: B 534 MET cc_start: 0.8240 (mtp) cc_final: 0.7932 (mtm) REVERT: B 1058 ARG cc_start: 0.4165 (OUTLIER) cc_final: 0.3856 (mpt-90) REVERT: B 1242 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7433 (m-80) outliers start: 18 outliers final: 12 residues processed: 50 average time/residue: 1.2688 time to fit residues: 71.4857 Evaluate side-chains 45 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 690 ASN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1058 ARG Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1216 SER Chi-restraints excluded: chain B residue 1242 TYR Chi-restraints excluded: chain B residue 1284 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.0770 chunk 35 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 116 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050919 restraints weight = 39334.674| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.80 r_work: 0.2775 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14481 Z= 0.192 Angle : 0.437 9.027 20146 Z= 0.233 Chirality : 0.035 0.142 2305 Planarity : 0.003 0.037 2070 Dihedral : 17.662 98.676 3387 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.32 % Allowed : 13.41 % Favored : 85.26 % 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: 1.39 (0.24), residues: 1339 helix: 1.97 (0.20), residues: 691 sheet: -0.61 (0.48), residues: 115 loop : -0.03 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 476 HIS 0.003 0.001 HIS B 328 PHE 0.009 0.001 PHE B1204 TYR 0.027 0.001 TYR B1013 ARG 0.004 0.000 ARG B 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3048.23 seconds wall clock time: 55 minutes 52.25 seconds (3352.25 seconds total)