Starting phenix.real_space_refine on Thu Aug 6 09:09:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2026/9ua2_63976.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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 127 5.49 5 Mg 4 5.21 5 S 37 5.16 5 C 8440 2.51 5 N 2507 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14114 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1408, 11415 Classifications: {'peptide': 1408} Link IDs: {'PTRANS': 38, 'TRANS': 1369} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2347 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 54, 'rna3p_pyr': 39} Link IDs: {'rna2p': 17, 'rna3p': 92} Chain: "C" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 187 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} 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} Time building chain proxies: 3.24, per 1000 atoms: 0.23 Number of scatterers: 14114 At special positions: 0 Unit cell: (93.93, 107.88, 143.22, 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 37 16.00 P 127 15.00 Mg 4 11.99 O 2999 8.00 N 2507 7.00 C 8440 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: 1.29 Conformation dependent library (CDL) restraints added in 626.0 milliseconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 54.4% alpha, 13.8% beta 36 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.799A pdb=" N VAL A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.600A pdb=" N GLN A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.542A pdb=" N THR A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.814A pdb=" N TYR A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 4.093A pdb=" N GLN A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.510A pdb=" N LEU A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.865A pdb=" N ILE A 320 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.573A pdb=" N ILE A 377 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 433 through 447 removed outlier: 4.543A pdb=" N ARG A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.575A pdb=" N VAL A 477 " --> pdb=" O TRP A 474 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 4.000A pdb=" N ARG A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 528 through 540 removed outlier: 3.939A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 4.032A pdb=" N LEU A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 removed outlier: 5.580A pdb=" N ILE A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.619A pdb=" N ALA A 603 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 604 " --> pdb=" O SER A 601 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 605 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR A 606 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 607 " --> pdb=" O GLN A 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 608 " --> pdb=" O LEU A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 608' Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 651 through 675 Processing helix chain 'A' and resid 693 through 702 removed outlier: 3.869A pdb=" N SER A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 3.606A pdb=" N LYS A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 732 removed outlier: 3.577A pdb=" N ASP A 731 " --> pdb=" O TRP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 812 through 825 removed outlier: 3.773A pdb=" N SER A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.704A pdb=" N GLN A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 838 removed outlier: 3.512A pdb=" N LEU A 838 " --> pdb=" O PHE A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 838' Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 875 through 893 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 912 through 920 Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 941 through 958 removed outlier: 3.995A pdb=" N ALA A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 972 through 981 Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 3.929A pdb=" N LEU A1049 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1088 Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1135 Processing helix chain 'A' and resid 1143 through 1147 removed outlier: 3.690A pdb=" N GLY A1147 " --> pdb=" O ASN A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1166 removed outlier: 4.043A pdb=" N GLU A1160 " --> pdb=" O PRO A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1198 Processing helix chain 'A' and resid 1269 through 1272 Processing helix chain 'A' and resid 1325 through 1332 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.827A pdb=" N GLN A1361 " --> pdb=" O VAL A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1366 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1392 through 1410 removed outlier: 3.575A pdb=" N GLN A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 910 removed outlier: 3.577A pdb=" N GLU A 690 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 15 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN A1372 " --> pdb=" O CYS A1387 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N CYS A1387 " --> pdb=" O GLN A1372 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS A1383 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU A1378 " --> pdb=" O THR A1381 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR A1381 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL A1307 " --> pdb=" O VAL A1298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 903 through 910 removed outlier: 3.577A pdb=" N GLU A 690 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 15 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ILE A1376 " --> pdb=" O LEU A 990 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 4.177A pdb=" N LYS A 492 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 754 through 757 Processing sheet with id=AA6, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 6.226A pdb=" N ASN A1110 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE A1014 " --> pdb=" O ASN A1110 " (cutoff:3.500A) removed outlier: 13.386A pdb=" N SER A1112 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 18.535A pdb=" N GLU A1012 " --> pdb=" O SER A1112 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET A1243 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY A1013 " --> pdb=" O LEU A1241 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A1241 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N PHE A1015 " --> pdb=" O TYR A1239 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N TYR A1239 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 13.378A pdb=" N GLU A1017 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 15.507A pdb=" N ASP A1237 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1040 through 1042 Processing sheet with id=AA8, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA9, first strand: chain 'A' and resid 1137 through 1142 Processing sheet with id=AB1, first strand: chain 'A' and resid 1266 through 1267 removed outlier: 7.645A pdb=" N LEU A1266 " --> pdb=" O LYS A1250 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 1.72 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: 3544 1.33 - 1.45: 3452 1.45 - 1.58: 7330 1.58 - 1.70: 251 1.70 - 1.82: 57 Bond restraints: 14634 Sorted by residual: bond pdb=" C3' DG C 6 " pdb=" C2' DG C 6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.54e+00 bond pdb=" C3' DC D 6 " pdb=" C2' DC D 6 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.20e+00 bond pdb=" C1' DC C 8 " pdb=" N1 DC C 8 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.82e+00 bond pdb=" C3' DA D 5 " pdb=" C2' DA D 5 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.42e+00 bond pdb=" C3' DG C 3 " pdb=" C2' DG C 3 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.10e+00 ... (remaining 14629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19818 2.17 - 4.34: 491 4.34 - 6.50: 22 6.50 - 8.67: 7 8.67 - 10.84: 3 Bond angle restraints: 20341 Sorted by residual: angle pdb=" O5' U B 47 " pdb=" C5' U B 47 " pdb=" C4' U B 47 " ideal model delta sigma weight residual 109.40 114.97 -5.57 8.00e-01 1.56e+00 4.85e+01 angle pdb=" C1' C B 55 " pdb=" N1 C B 55 " pdb=" C2 C B 55 " ideal model delta sigma weight residual 118.80 125.01 -6.21 1.10e+00 8.26e-01 3.19e+01 angle pdb=" C3' A B 60 " pdb=" O3' A B 60 " pdb=" P A B 61 " ideal model delta sigma weight residual 119.70 125.52 -5.82 1.20e+00 6.94e-01 2.35e+01 angle pdb=" O2 C B 55 " pdb=" C2 C B 55 " pdb=" N3 C B 55 " ideal model delta sigma weight residual 121.90 118.58 3.32 7.00e-01 2.04e+00 2.25e+01 angle pdb=" N7 G B 44 " pdb=" C5 G B 44 " pdb=" C6 G B 44 " ideal model delta sigma weight residual 130.40 127.80 2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 20336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 8496 35.95 - 71.91: 434 71.91 - 107.86: 39 107.86 - 143.82: 5 143.82 - 179.77: 7 Dihedral angle restraints: 8981 sinusoidal: 4835 harmonic: 4146 Sorted by residual: dihedral pdb=" O4' C B 55 " pdb=" C1' C B 55 " pdb=" N1 C B 55 " pdb=" C2 C B 55 " ideal model delta sinusoidal sigma weight residual -160.00 17.05 -177.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 90 " pdb=" C1' U B 90 " pdb=" N1 U B 90 " pdb=" C2 U B 90 " ideal model delta sinusoidal sigma weight residual 200.00 45.42 154.58 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" O4' U B 64 " pdb=" C1' U B 64 " pdb=" N1 U B 64 " pdb=" C2 U B 64 " ideal model delta sinusoidal sigma weight residual 200.00 48.29 151.71 1 1.50e+01 4.44e-03 8.02e+01 ... (remaining 8978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1827 0.050 - 0.100: 362 0.100 - 0.151: 146 0.151 - 0.201: 11 0.201 - 0.251: 3 Chirality restraints: 2349 Sorted by residual: chirality pdb=" C1' G B 51 " pdb=" O4' G B 51 " pdb=" C2' G B 51 " pdb=" N9 G B 51 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P U B 47 " pdb=" OP1 U B 47 " pdb=" OP2 U B 47 " pdb=" O5' U B 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' C B 116 " pdb=" C4' C B 116 " pdb=" O3' C B 116 " pdb=" C2' C B 116 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2346 not shown) Planarity restraints: 2138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 528 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C SER A 528 " 0.067 2.00e-02 2.50e+03 pdb=" O SER A 528 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 529 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 99 " -0.029 2.00e-02 2.50e+03 1.25e-02 4.72e+00 pdb=" N9 G B 99 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G B 99 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 99 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 99 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 99 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 99 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G B 99 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 99 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 99 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 99 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 99 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 49 " 0.022 2.00e-02 2.50e+03 9.80e-03 2.64e+00 pdb=" N9 A B 49 " -0.023 2.00e-02 2.50e+03 pdb=" C8 A B 49 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 49 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 49 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 49 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 49 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 49 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 49 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 49 " -0.003 2.00e-02 2.50e+03 ... (remaining 2135 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1296 2.74 - 3.28: 14160 3.28 - 3.82: 25286 3.82 - 4.36: 31322 4.36 - 4.90: 48878 Nonbonded interactions: 120942 Sorted by model distance: nonbonded pdb=" OG1 THR A 54 " pdb=" OP2 A B 16 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 420 " pdb=" OD2 ASP A 446 " model vdw 2.214 3.040 nonbonded pdb=" OD2 ASP A 369 " pdb=" OH TYR A 402 " model vdw 2.232 3.040 nonbonded pdb=" O2' C B 43 " pdb=" OP1 G B 44 " model vdw 2.241 3.040 nonbonded pdb=" O2' C B 116 " pdb=" OP1 C B 117 " model vdw 2.258 3.040 ... (remaining 120937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:9.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.003 0.037 14634 Z= 0.198 Angle : 0.679 10.840 20341 Z= 0.486 Chirality : 0.049 0.251 2349 Planarity : 0.004 0.047 2138 Dihedral : 19.477 179.772 6293 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.62 % Favored : 95.09 % Rotamer: Outliers : 0.40 % Allowed : 12.83 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1406 helix: 0.22 (0.21), residues: 647 sheet: -0.02 (0.44), residues: 129 loop : -0.67 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 409 TYR 0.021 0.002 TYR A 463 PHE 0.012 0.001 PHE A 835 TRP 0.017 0.001 TRP A 338 HIS 0.003 0.001 HIS A1018 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.20 (14634) covalent geometry : angle 0.67891 / 0.49 (20341) hydrogen bonds : bond 0.14184 / 9.53 ( 633) hydrogen bonds : angle 6.76563 / 4.78 ( 1793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.7032 (t70) cc_final: 0.6719 (t70) REVERT: A 297 VAL cc_start: 0.8276 (t) cc_final: 0.8041 (m) REVERT: A 460 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.6851 (ttm-80) REVERT: A 767 TYR cc_start: 0.6216 (m-80) cc_final: 0.5903 (m-10) REVERT: A 773 ASN cc_start: 0.6962 (t0) cc_final: 0.6540 (t0) REVERT: A 947 ASP cc_start: 0.7006 (m-30) cc_final: 0.6509 (m-30) REVERT: A 1381 THR cc_start: 0.8098 (t) cc_final: 0.7843 (m) outliers start: 5 outliers final: 2 residues processed: 122 average time/residue: 0.5592 time to fit residues: 75.7573 Evaluate side-chains 104 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 661 GLN A1121 ASN A1406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.202347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155185 restraints weight = 14788.430| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.83 r_work: 0.3495 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14634 Z= 0.240 Angle : 0.658 8.693 20341 Z= 0.358 Chirality : 0.046 0.407 2349 Planarity : 0.005 0.055 2138 Dihedral : 20.624 178.422 3401 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.81 % Rotamer: Outliers : 2.79 % Allowed : 11.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.22), residues: 1406 helix: 0.06 (0.20), residues: 662 sheet: -0.18 (0.44), residues: 128 loop : -0.78 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 384 TYR 0.016 0.002 TYR A 281 PHE 0.019 0.002 PHE A1339 TRP 0.017 0.002 TRP A 352 HIS 0.007 0.002 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (14634) covalent geometry : angle 0.65784 / 0.36 (20341) hydrogen bonds : bond 0.05083 / 3.49 ( 633) hydrogen bonds : angle 5.32871 / 3.73 ( 1793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6588 (tppt) REVERT: A 191 MET cc_start: -0.1250 (OUTLIER) cc_final: -0.2513 (ptp) REVERT: A 234 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7928 (m) REVERT: A 289 ASP cc_start: 0.7047 (t70) cc_final: 0.6774 (t70) REVERT: A 460 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.6880 (ttm-80) REVERT: A 767 TYR cc_start: 0.6259 (m-80) cc_final: 0.5931 (m-10) REVERT: A 768 MET cc_start: 0.7508 (mtm) cc_final: 0.7159 (mtm) REVERT: A 773 ASN cc_start: 0.7072 (t0) cc_final: 0.6682 (t0) REVERT: A 779 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5269 (tp) REVERT: A 891 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: A 947 ASP cc_start: 0.7236 (m-30) cc_final: 0.6940 (m-30) REVERT: A 959 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7298 (ttt90) REVERT: A 1034 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: A 1145 ARG cc_start: 0.7762 (mtm-85) cc_final: 0.7348 (mtp180) REVERT: A 1198 ARG cc_start: 0.7167 (tmm160) cc_final: 0.6399 (tpt170) outliers start: 35 outliers final: 12 residues processed: 131 average time/residue: 0.5316 time to fit residues: 77.6056 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1034 ASP Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1362 MET Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 928 ASN A1121 ASN A1372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.205677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159702 restraints weight = 14740.312| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.84 r_work: 0.3533 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14634 Z= 0.145 Angle : 0.558 7.628 20341 Z= 0.310 Chirality : 0.041 0.347 2349 Planarity : 0.004 0.041 2138 Dihedral : 20.637 179.156 3401 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.91 % Favored : 94.88 % Rotamer: Outliers : 2.07 % Allowed : 13.63 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1406 helix: 0.27 (0.20), residues: 657 sheet: -0.33 (0.44), residues: 130 loop : -0.72 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.016 0.001 TYR A 281 PHE 0.013 0.001 PHE A1339 TRP 0.015 0.001 TRP A 352 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (14634) covalent geometry : angle 0.55770 / 0.31 (20341) hydrogen bonds : bond 0.04436 / 3.02 ( 633) hydrogen bonds : angle 4.98161 / 3.48 ( 1793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6533 (tppt) REVERT: A 271 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 289 ASP cc_start: 0.6995 (t70) cc_final: 0.6739 (t70) REVERT: A 460 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.6894 (ttm-80) REVERT: A 767 TYR cc_start: 0.6221 (m-80) cc_final: 0.5916 (m-10) REVERT: A 768 MET cc_start: 0.7534 (mtm) cc_final: 0.7187 (mtm) REVERT: A 773 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6586 (t0) REVERT: A 779 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5682 (tp) REVERT: A 947 ASP cc_start: 0.7191 (m-30) cc_final: 0.6606 (m-30) REVERT: A 959 ARG cc_start: 0.7546 (ttt90) cc_final: 0.7160 (tpt-90) REVERT: A 963 ASN cc_start: 0.7536 (m110) cc_final: 0.7161 (m-40) REVERT: A 1145 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7462 (mtp180) REVERT: A 1335 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6220 (pt) outliers start: 26 outliers final: 9 residues processed: 129 average time/residue: 0.4972 time to fit residues: 71.3357 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 773 ASN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1372 GLN Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 44 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 918 GLN A 928 ASN A1121 ASN A1372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.205510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158950 restraints weight = 14850.004| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.76 r_work: 0.3556 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14634 Z= 0.142 Angle : 0.548 7.410 20341 Z= 0.304 Chirality : 0.041 0.349 2349 Planarity : 0.004 0.041 2138 Dihedral : 20.621 179.156 3401 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.05 % Favored : 94.74 % Rotamer: Outliers : 2.63 % Allowed : 13.71 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1406 helix: 0.35 (0.20), residues: 663 sheet: -0.44 (0.43), residues: 131 loop : -0.75 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.016 0.001 TYR A1117 PHE 0.013 0.001 PHE A1339 TRP 0.014 0.001 TRP A 352 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14634) covalent geometry : angle 0.54824 / 0.30 (20341) hydrogen bonds : bond 0.04218 / 2.87 ( 633) hydrogen bonds : angle 4.84932 / 3.38 ( 1793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6544 (tppt) REVERT: A 271 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 289 ASP cc_start: 0.6947 (t70) cc_final: 0.6698 (t70) REVERT: A 460 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.6824 (ttm-80) REVERT: A 732 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5462 (tt0) REVERT: A 767 TYR cc_start: 0.6168 (m-80) cc_final: 0.5851 (m-10) REVERT: A 768 MET cc_start: 0.7481 (mtm) cc_final: 0.7072 (mtm) REVERT: A 779 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5667 (tp) REVERT: A 863 ILE cc_start: 0.4852 (OUTLIER) cc_final: 0.4646 (mp) REVERT: A 947 ASP cc_start: 0.7100 (m-30) cc_final: 0.6500 (m-30) REVERT: A 959 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7122 (tpt-90) REVERT: A 963 ASN cc_start: 0.7521 (m110) cc_final: 0.7197 (m-40) REVERT: A 1034 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: A 1145 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7440 (mtp180) REVERT: A 1298 VAL cc_start: 0.7752 (t) cc_final: 0.7453 (t) REVERT: A 1335 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6091 (pt) outliers start: 33 outliers final: 13 residues processed: 128 average time/residue: 0.5156 time to fit residues: 73.4114 Evaluate side-chains 117 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 929 LYS Chi-restraints excluded: chain A residue 1034 ASP Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1394 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 145 optimal weight: 8.9990 chunk 30 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 870 ASN A 918 GLN A 928 ASN A1121 ASN A1245 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161205 restraints weight = 14826.177| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.74 r_work: 0.3584 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14634 Z= 0.118 Angle : 0.517 7.448 20341 Z= 0.287 Chirality : 0.039 0.350 2349 Planarity : 0.003 0.039 2138 Dihedral : 20.606 179.633 3401 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 2.55 % Allowed : 14.26 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1406 helix: 0.49 (0.20), residues: 664 sheet: -0.53 (0.43), residues: 130 loop : -0.73 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1145 TYR 0.019 0.001 TYR A1117 PHE 0.010 0.001 PHE A1339 TRP 0.013 0.001 TRP A 352 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (14634) covalent geometry : angle 0.51711 / 0.29 (20341) hydrogen bonds : bond 0.03979 / 2.71 ( 633) hydrogen bonds : angle 4.66967 / 3.25 ( 1793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6461 (tppt) REVERT: A 271 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 289 ASP cc_start: 0.6871 (t70) cc_final: 0.6643 (t70) REVERT: A 460 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.6791 (ttm-80) REVERT: A 732 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5388 (tt0) REVERT: A 767 TYR cc_start: 0.6155 (m-80) cc_final: 0.5865 (m-80) REVERT: A 768 MET cc_start: 0.7442 (mtm) cc_final: 0.7055 (mtm) REVERT: A 779 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5701 (tp) REVERT: A 947 ASP cc_start: 0.7054 (m-30) cc_final: 0.6548 (m-30) REVERT: A 959 ARG cc_start: 0.7343 (ttt90) cc_final: 0.7009 (tpt-90) REVERT: A 963 ASN cc_start: 0.7413 (m110) cc_final: 0.7081 (m-40) REVERT: A 1145 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7480 (mtp180) REVERT: A 1198 ARG cc_start: 0.6982 (tmm160) cc_final: 0.6228 (tpt170) REVERT: A 1335 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5955 (pt) outliers start: 32 outliers final: 13 residues processed: 129 average time/residue: 0.5006 time to fit residues: 72.1430 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1394 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 918 GLN A 928 ASN A1121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156210 restraints weight = 14894.087| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.72 r_work: 0.3544 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14634 Z= 0.174 Angle : 0.557 8.416 20341 Z= 0.303 Chirality : 0.041 0.350 2349 Planarity : 0.004 0.043 2138 Dihedral : 20.556 179.616 3399 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.55 % Favored : 94.24 % Rotamer: Outliers : 2.79 % Allowed : 14.74 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1406 helix: 0.44 (0.20), residues: 664 sheet: -0.62 (0.42), residues: 131 loop : -0.74 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.019 0.001 TYR A1117 PHE 0.019 0.001 PHE A1339 TRP 0.011 0.001 TRP A 352 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14634) covalent geometry : angle 0.55702 / 0.30 (20341) hydrogen bonds : bond 0.04166 / 2.84 ( 633) hydrogen bonds : angle 4.70732 / 3.27 ( 1793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6532 (tppt) REVERT: A 271 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 440 GLN cc_start: 0.4782 (tt0) cc_final: 0.4156 (tm-30) REVERT: A 460 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.6717 (ttm-80) REVERT: A 732 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5519 (tt0) REVERT: A 767 TYR cc_start: 0.6182 (m-80) cc_final: 0.5871 (m-80) REVERT: A 768 MET cc_start: 0.7507 (mtm) cc_final: 0.7141 (mtm) REVERT: A 773 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6565 (t160) REVERT: A 779 ILE cc_start: 0.5925 (OUTLIER) cc_final: 0.5476 (tp) REVERT: A 947 ASP cc_start: 0.7098 (m-30) cc_final: 0.6481 (m-30) REVERT: A 959 ARG cc_start: 0.7318 (ttt90) cc_final: 0.7007 (tpt-90) REVERT: A 963 ASN cc_start: 0.7340 (m110) cc_final: 0.7015 (m-40) REVERT: A 1198 ARG cc_start: 0.6980 (tmm160) cc_final: 0.6169 (tpt170) REVERT: A 1335 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5915 (pt) outliers start: 35 outliers final: 16 residues processed: 132 average time/residue: 0.5386 time to fit residues: 79.2551 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 773 ASN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 928 ASN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.203545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155034 restraints weight = 14802.500| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.79 r_work: 0.3529 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14634 Z= 0.182 Angle : 0.566 9.801 20341 Z= 0.308 Chirality : 0.042 0.351 2349 Planarity : 0.004 0.045 2138 Dihedral : 20.552 179.621 3399 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.48 % Favored : 94.31 % Rotamer: Outliers : 2.87 % Allowed : 14.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1406 helix: 0.40 (0.20), residues: 664 sheet: -0.75 (0.41), residues: 131 loop : -0.77 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 384 TYR 0.021 0.002 TYR A1117 PHE 0.018 0.001 PHE A1339 TRP 0.012 0.001 TRP A 352 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (14634) covalent geometry : angle 0.56616 / 0.31 (20341) hydrogen bonds : bond 0.04240 / 2.90 ( 633) hydrogen bonds : angle 4.72341 / 3.28 ( 1793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6529 (tppt) REVERT: A 237 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: A 271 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 440 GLN cc_start: 0.4813 (tt0) cc_final: 0.4177 (tm-30) REVERT: A 460 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.6666 (ttm-80) REVERT: A 732 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5461 (tt0) REVERT: A 767 TYR cc_start: 0.6139 (m-80) cc_final: 0.5803 (m-80) REVERT: A 768 MET cc_start: 0.7517 (mtm) cc_final: 0.7125 (mtm) REVERT: A 773 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6428 (t0) REVERT: A 779 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5489 (tp) REVERT: A 947 ASP cc_start: 0.7103 (m-30) cc_final: 0.6751 (m-30) REVERT: A 959 ARG cc_start: 0.7326 (ttt90) cc_final: 0.6984 (tpt-90) REVERT: A 963 ASN cc_start: 0.7318 (m110) cc_final: 0.6970 (m-40) REVERT: A 1198 ARG cc_start: 0.6991 (tmm160) cc_final: 0.6153 (tpt170) REVERT: A 1335 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5888 (pt) outliers start: 36 outliers final: 16 residues processed: 127 average time/residue: 0.4847 time to fit residues: 68.7455 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 773 ASN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 144 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 928 ASN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.202932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154320 restraints weight = 14851.399| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.77 r_work: 0.3522 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14634 Z= 0.195 Angle : 0.576 9.445 20341 Z= 0.313 Chirality : 0.042 0.351 2349 Planarity : 0.004 0.046 2138 Dihedral : 20.544 179.598 3399 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.48 % Favored : 94.31 % Rotamer: Outliers : 2.87 % Allowed : 14.58 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1406 helix: 0.34 (0.20), residues: 665 sheet: -0.82 (0.41), residues: 131 loop : -0.78 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 384 TYR 0.022 0.002 TYR A1117 PHE 0.019 0.002 PHE A1339 TRP 0.012 0.001 TRP A 352 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (14634) covalent geometry : angle 0.57580 / 0.31 (20341) hydrogen bonds : bond 0.04296 / 2.93 ( 633) hydrogen bonds : angle 4.74038 / 3.29 ( 1793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6558 (tppt) REVERT: A 237 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: A 271 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 440 GLN cc_start: 0.4754 (tt0) cc_final: 0.4134 (tm-30) REVERT: A 460 ARG cc_start: 0.7560 (ttp-170) cc_final: 0.6664 (ttm-80) REVERT: A 685 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7849 (tt) REVERT: A 732 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5086 (tt0) REVERT: A 767 TYR cc_start: 0.6172 (m-80) cc_final: 0.5842 (m-80) REVERT: A 768 MET cc_start: 0.7496 (mtm) cc_final: 0.7082 (mtm) REVERT: A 779 ILE cc_start: 0.5890 (OUTLIER) cc_final: 0.5422 (tp) REVERT: A 947 ASP cc_start: 0.7107 (m-30) cc_final: 0.6777 (m-30) REVERT: A 959 ARG cc_start: 0.7331 (ttt90) cc_final: 0.6999 (tpt-90) REVERT: A 963 ASN cc_start: 0.7287 (m110) cc_final: 0.6957 (m-40) REVERT: A 1012 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 1150 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7651 (mmtm) REVERT: A 1198 ARG cc_start: 0.6982 (tmm160) cc_final: 0.6181 (tpt170) REVERT: A 1335 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5883 (pt) outliers start: 36 outliers final: 18 residues processed: 132 average time/residue: 0.5260 time to fit residues: 77.0863 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1150 LYS Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 773 ASN A 928 ASN A1121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.205297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157974 restraints weight = 14945.862| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.68 r_work: 0.3556 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14634 Z= 0.133 Angle : 0.538 11.063 20341 Z= 0.296 Chirality : 0.039 0.351 2349 Planarity : 0.004 0.042 2138 Dihedral : 20.528 179.862 3399 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.52 % Rotamer: Outliers : 2.23 % Allowed : 15.54 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1406 helix: 0.43 (0.20), residues: 665 sheet: -0.83 (0.41), residues: 130 loop : -0.79 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.024 0.001 TYR A1117 PHE 0.012 0.001 PHE A1339 TRP 0.014 0.001 TRP A 352 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14634) covalent geometry : angle 0.53837 / 0.30 (20341) hydrogen bonds : bond 0.04032 / 2.74 ( 633) hydrogen bonds : angle 4.61851 / 3.21 ( 1793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6539 (tppt) REVERT: A 271 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 440 GLN cc_start: 0.4926 (tt0) cc_final: 0.4216 (tm-30) REVERT: A 460 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.6767 (ttm-80) REVERT: A 685 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7864 (tt) REVERT: A 767 TYR cc_start: 0.6195 (m-80) cc_final: 0.5881 (m-80) REVERT: A 768 MET cc_start: 0.7545 (mtm) cc_final: 0.7113 (mtm) REVERT: A 779 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5750 (tp) REVERT: A 947 ASP cc_start: 0.7133 (m-30) cc_final: 0.6510 (m-30) REVERT: A 959 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6800 (tpp80) REVERT: A 963 ASN cc_start: 0.7280 (m110) cc_final: 0.6778 (m110) REVERT: A 1150 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7676 (mmtm) REVERT: A 1198 ARG cc_start: 0.6999 (tmm160) cc_final: 0.6245 (tpt170) REVERT: A 1335 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5861 (pt) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 0.5276 time to fit residues: 73.7959 Evaluate side-chains 120 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1150 LYS Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 928 ASN A1121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155296 restraints weight = 14833.607| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.87 r_work: 0.3525 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14634 Z= 0.180 Angle : 0.572 11.137 20341 Z= 0.310 Chirality : 0.042 0.350 2349 Planarity : 0.004 0.046 2138 Dihedral : 20.499 179.454 3399 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 2.07 % Allowed : 15.78 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1406 helix: 0.35 (0.20), residues: 665 sheet: -0.87 (0.41), residues: 131 loop : -0.81 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.026 0.002 TYR A1117 PHE 0.018 0.001 PHE A1339 TRP 0.013 0.001 TRP A 352 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (14634) covalent geometry : angle 0.57236 / 0.31 (20341) hydrogen bonds : bond 0.04223 / 2.88 ( 633) hydrogen bonds : angle 4.67284 / 3.24 ( 1793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6554 (tppt) REVERT: A 237 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: A 271 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 440 GLN cc_start: 0.4720 (tt0) cc_final: 0.4088 (tm-30) REVERT: A 732 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5750 (tt0) REVERT: A 767 TYR cc_start: 0.6190 (m-80) cc_final: 0.5860 (m-80) REVERT: A 779 ILE cc_start: 0.5879 (OUTLIER) cc_final: 0.5426 (tp) REVERT: A 947 ASP cc_start: 0.7106 (m-30) cc_final: 0.6771 (m-30) REVERT: A 959 ARG cc_start: 0.7305 (ttt90) cc_final: 0.6985 (tpt-90) REVERT: A 963 ASN cc_start: 0.7168 (m110) cc_final: 0.6831 (m-40) REVERT: A 1133 ASP cc_start: 0.8205 (m-30) cc_final: 0.7661 (t0) REVERT: A 1150 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.7614 (mmtm) REVERT: A 1198 ARG cc_start: 0.6986 (tmm160) cc_final: 0.6171 (tpt170) REVERT: A 1335 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5767 (pt) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 0.5455 time to fit residues: 74.6657 Evaluate side-chains 121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1150 LYS Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 97 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 928 ASN A1121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.202895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154425 restraints weight = 14872.252| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.76 r_work: 0.3527 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14634 Z= 0.182 Angle : 0.577 11.210 20341 Z= 0.313 Chirality : 0.042 0.350 2349 Planarity : 0.004 0.047 2138 Dihedral : 20.504 179.618 3399 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.52 % Rotamer: Outliers : 2.31 % Allowed : 15.54 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.22), residues: 1406 helix: 0.30 (0.20), residues: 666 sheet: -0.88 (0.40), residues: 131 loop : -0.83 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 384 TYR 0.025 0.002 TYR A1117 PHE 0.018 0.002 PHE A1339 TRP 0.011 0.001 TRP A 352 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (14634) covalent geometry : angle 0.57666 / 0.31 (20341) hydrogen bonds : bond 0.04238 / 2.89 ( 633) hydrogen bonds : angle 4.69255 / 3.26 ( 1793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.20 seconds wall clock time: 83 minutes 8.75 seconds (4988.75 seconds total)