Starting phenix.real_space_refine on Sat Aug 23 20:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ua2_63976/08_2025/9ua2_63976.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ua2_63976/08_2025/9ua2_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_2025/9ua2_63976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2025/9ua2_63976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2025/9ua2_63976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ua2_63976/08_2025/9ua2_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-2.0-5787/lib/python3.9/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: 2.67, per 1000 atoms: 0.19 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: 0.82 Conformation dependent library (CDL) restraints added in 399.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.74 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: 3.23 Time building geometry restraints manager: 1.10 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: 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' A B 60 " pdb=" O3' A B 60 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.22e+00 bond pdb=" C3' A B 40 " pdb=" O3' A B 40 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.15e+00 bond pdb=" C3' C B 43 " pdb=" O3' C B 43 " ideal model delta sigma weight residual 1.417 1.432 -0.015 1.50e-02 4.44e+03 9.99e-01 bond pdb=" CG LEU A 401 " pdb=" CD2 LEU A 401 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.22e-01 bond pdb=" CB GLN A 918 " pdb=" CG GLN A 918 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.93e-01 ... (remaining 14629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 20056 2.17 - 4.34: 256 4.34 - 6.50: 19 6.50 - 8.67: 7 8.67 - 10.84: 3 Bond angle restraints: 20341 Sorted by residual: angle pdb=" OP1 U B 47 " pdb=" P U B 47 " pdb=" OP2 U B 47 " ideal model delta sigma weight residual 119.60 108.76 10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C3' A B 60 " pdb=" O3' A B 60 " pdb=" P A B 61 " ideal model delta sigma weight residual 120.20 125.52 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C ARG A 527 " pdb=" N SER A 528 " pdb=" CA SER A 528 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" OP1 C B 117 " pdb=" P C B 117 " pdb=" OP2 C B 117 " ideal model delta sigma weight residual 119.60 110.29 9.31 3.00e+00 1.11e-01 9.63e+00 angle pdb=" O3' A B 46 " pdb=" C3' A B 46 " pdb=" C2' A B 46 " ideal model delta sigma weight residual 113.70 118.24 -4.54 1.50e+00 4.44e-01 9.15e+00 ... (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 - 0.048: 1925 0.048 - 0.095: 351 0.095 - 0.143: 62 0.143 - 0.190: 7 0.190 - 0.238: 4 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 2.46 2.22 0.24 2.00e-01 2.50e+01 1.41e+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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.032 14634 Z= 0.126 Angle : 0.602 10.840 20341 Z= 0.316 Chirality : 0.039 0.238 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 aren 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 covalent geometry : bond 0.00262 (14634) covalent geometry : angle 0.60175 (20341) hydrogen bonds : bond 0.14184 ( 633) hydrogen bonds : angle 6.76563 ( 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 : 0.465 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: 0.7007 (m-30) cc_final: 0.6509 (m-30) REVERT: A 1381 THR cc_start: 0.8098 (t) cc_final: 0.7842 (m) outliers start: 5 outliers final: 2 residues processed: 122 average time/residue: 0.4565 time to fit residues: 61.9673 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 : 0.316 ------------------------------------------------------------------------------- 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: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4232 r_free = 0.4232 target = 0.201206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154360 restraints weight = 14789.309| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.89 r_work: 0.3478 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14634 Z= 0.262 Angle : 0.668 7.941 20341 Z= 0.354 Chirality : 0.045 0.312 2349 Planarity : 0.005 0.046 2138 Dihedral : 20.604 177.120 3401 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 3.11 % Allowed : 11.55 % Favored : 85.34 % 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 aren not related in a simple way. whole: -0.57 (0.22), residues: 1406 helix: 0.03 (0.20), residues: 662 sheet: -0.10 (0.44), residues: 128 loop : -0.76 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 384 TYR 0.017 0.002 TYR A 281 PHE 0.021 0.002 PHE A 650 TRP 0.017 0.002 TRP A 352 HIS 0.007 0.002 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00582 (14634) covalent geometry : angle 0.66818 (20341) hydrogen bonds : bond 0.04818 ( 633) hydrogen bonds : angle 5.25421 ( 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 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6623 (tppt) REVERT: A 191 MET cc_start: -0.1224 (OUTLIER) cc_final: -0.2509 (ptp) REVERT: A 271 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 289 ASP cc_start: 0.7064 (t70) cc_final: 0.6791 (t70) REVERT: A 460 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.6915 (ttm-80) REVERT: A 685 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 767 TYR cc_start: 0.6276 (m-80) cc_final: 0.5934 (m-10) REVERT: A 768 MET cc_start: 0.7516 (mtm) cc_final: 0.7158 (mtm) REVERT: A 773 ASN cc_start: 0.7124 (t0) cc_final: 0.6783 (t0) REVERT: A 779 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5513 (tp) REVERT: A 947 ASP cc_start: 0.7304 (m-30) cc_final: 0.7041 (m-30) REVERT: A 959 ARG cc_start: 0.7578 (ttt90) cc_final: 0.7373 (ttt90) REVERT: A 1034 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: A 1094 MET cc_start: 0.8602 (mtp) cc_final: 0.8394 (mtp) REVERT: A 1292 MET cc_start: 0.9073 (mmt) cc_final: 0.8871 (mmt) outliers start: 39 outliers final: 14 residues processed: 132 average time/residue: 0.4486 time to fit residues: 66.0391 Evaluate side-chains 115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 685 LEU 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 1168 SER Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1309 MET 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: 6.9990 chunk 68 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4255 r_free = 0.4255 target = 0.203692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156859 restraints weight = 14748.150| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.80 r_work: 0.3520 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1245 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 : 0.589 7.219 20341 Z= 0.314 Chirality : 0.041 0.285 2349 Planarity : 0.004 0.046 2138 Dihedral : 20.568 176.201 3401 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.81 % Rotamer: Outliers : 2.55 % Allowed : 13.15 % 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 aren not related in a simple way. whole: -0.48 (0.22), residues: 1406 helix: 0.21 (0.20), residues: 666 sheet: -0.29 (0.44), residues: 129 loop : -0.81 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.015 0.002 TYR A 281 PHE 0.014 0.001 PHE A1339 TRP 0.015 0.001 TRP A 352 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00378 (14634) covalent geometry : angle 0.58929 (20341) hydrogen bonds : bond 0.04101 ( 633) hydrogen bonds : angle 4.91947 ( 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 142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6588 (tppt) REVERT: A 234 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7845 (m) REVERT: A 271 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 289 ASP cc_start: 0.6985 (t70) cc_final: 0.6747 (t70) REVERT: A 460 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.6855 (ttm-80) REVERT: A 479 LYS cc_start: 0.8018 (tttp) cc_final: 0.7804 (tptp) REVERT: A 685 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 767 TYR cc_start: 0.6224 (m-80) cc_final: 0.5878 (m-10) REVERT: A 768 MET cc_start: 0.7522 (mtm) cc_final: 0.7170 (mtm) REVERT: A 773 ASN cc_start: 0.6994 (t0) cc_final: 0.6770 (t0) REVERT: A 779 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5677 (tp) REVERT: A 947 ASP cc_start: 0.7171 (m-30) cc_final: 0.6808 (m-30) REVERT: A 959 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7139 (tpt-90) REVERT: A 963 ASN cc_start: 0.7524 (m-40) cc_final: 0.7241 (m-40) REVERT: A 1034 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: A 1145 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7377 (mtp180) REVERT: A 1198 ARG cc_start: 0.7124 (tmm160) cc_final: 0.6350 (tpt170) REVERT: A 1292 MET cc_start: 0.9051 (mmt) cc_final: 0.8849 (mmt) REVERT: A 1335 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6163 (pt) outliers start: 32 outliers final: 9 residues processed: 131 average time/residue: 0.4222 time to fit residues: 61.6685 Evaluate side-chains 114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 646 THR Chi-restraints excluded: chain A residue 685 LEU 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 1168 SER Chi-restraints excluded: chain A residue 1196 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 44 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 918 GLN A 928 ASN A1121 ASN A1245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.206430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157661 restraints weight = 14935.608| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.89 r_work: 0.3577 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1474 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= 0.134 Angle : 0.548 7.021 20341 Z= 0.291 Chirality : 0.039 0.271 2349 Planarity : 0.004 0.044 2138 Dihedral : 20.489 177.074 3399 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 2.87 % Allowed : 13.63 % Favored : 83.51 % 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 aren not related in a simple way. whole: -0.33 (0.22), residues: 1406 helix: 0.44 (0.20), residues: 664 sheet: -0.47 (0.43), residues: 131 loop : -0.80 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.017 0.001 TYR A1117 PHE 0.010 0.001 PHE A1339 TRP 0.014 0.001 TRP A 352 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00282 (14634) covalent geometry : angle 0.54771 (20341) hydrogen bonds : bond 0.03687 ( 633) hydrogen bonds : angle 4.64667 ( 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 146 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6492 (tppt) REVERT: A 234 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7641 (m) REVERT: A 271 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 460 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.6679 (ttm-80) REVERT: A 479 LYS cc_start: 0.8064 (tttp) cc_final: 0.7755 (tptp) REVERT: A 732 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: A 767 TYR cc_start: 0.6099 (m-80) cc_final: 0.5788 (m-10) REVERT: A 779 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5469 (tp) REVERT: A 947 ASP cc_start: 0.6976 (m-30) cc_final: 0.6381 (m-30) REVERT: A 959 ARG cc_start: 0.7223 (ttt90) cc_final: 0.6916 (tpt-90) REVERT: A 963 ASN cc_start: 0.7313 (m-40) cc_final: 0.6978 (m-40) REVERT: A 1145 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7447 (mtp180) REVERT: A 1198 ARG cc_start: 0.6916 (tmm160) cc_final: 0.6112 (tpt170) REVERT: A 1335 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5775 (pt) outliers start: 36 outliers final: 13 residues processed: 136 average time/residue: 0.4749 time to fit residues: 71.8296 Evaluate side-chains 116 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP 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 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 700 LEU Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 891 GLU 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 1372 GLN Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN 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 = 0.4257 r_free = 0.4257 target = 0.204066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.158225 restraints weight = 14781.211| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.73 r_work: 0.3527 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14634 Z= 0.168 Angle : 0.567 8.457 20341 Z= 0.299 Chirality : 0.040 0.281 2349 Planarity : 0.004 0.045 2138 Dihedral : 20.457 176.401 3399 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.38 % Rotamer: Outliers : 3.11 % Allowed : 14.26 % Favored : 82.63 % 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 aren not related in a simple way. whole: -0.35 (0.22), residues: 1406 helix: 0.45 (0.20), residues: 665 sheet: -0.54 (0.42), residues: 131 loop : -0.82 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.020 0.001 TYR A1117 PHE 0.016 0.001 PHE A1339 TRP 0.013 0.001 TRP A 352 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00367 (14634) covalent geometry : angle 0.56705 (20341) hydrogen bonds : bond 0.03797 ( 633) hydrogen bonds : angle 4.66871 ( 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 145 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6580 (tppt) REVERT: A 234 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7778 (m) REVERT: A 271 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 460 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.6873 (ttm-80) REVERT: A 732 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5661 (tt0) REVERT: A 767 TYR cc_start: 0.6234 (m-80) cc_final: 0.5928 (m-10) REVERT: A 768 MET cc_start: 0.7594 (mtm) cc_final: 0.7273 (mtm) REVERT: A 779 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5704 (tp) REVERT: A 947 ASP cc_start: 0.7087 (m-30) cc_final: 0.6699 (m-30) REVERT: A 959 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7169 (tpt-90) REVERT: A 963 ASN cc_start: 0.7491 (m-40) cc_final: 0.7187 (m-40) REVERT: A 1012 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: A 1145 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7586 (mtp180) REVERT: A 1150 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7783 (mmtm) REVERT: A 1198 ARG cc_start: 0.7105 (tmm160) cc_final: 0.6338 (tpt170) outliers start: 39 outliers final: 15 residues processed: 136 average time/residue: 0.5047 time to fit residues: 76.5999 Evaluate side-chains 123 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 646 THR 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 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1012 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 1372 GLN Chi-restraints excluded: chain A residue 1377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 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: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 918 GLN 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 = 0.4244 r_free = 0.4244 target = 0.202478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154566 restraints weight = 14898.194| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.81 r_work: 0.3514 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1763 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= 0.197 Angle : 0.591 8.847 20341 Z= 0.311 Chirality : 0.041 0.295 2349 Planarity : 0.004 0.047 2138 Dihedral : 20.444 176.366 3399 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.48 % Favored : 94.31 % Rotamer: Outliers : 3.19 % Allowed : 14.58 % 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 aren not related in a simple way. whole: -0.40 (0.22), residues: 1406 helix: 0.37 (0.20), residues: 665 sheet: -0.57 (0.41), residues: 129 loop : -0.81 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 384 TYR 0.023 0.002 TYR A1117 PHE 0.018 0.002 PHE A1339 TRP 0.012 0.001 TRP A 352 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00433 (14634) covalent geometry : angle 0.59138 (20341) hydrogen bonds : bond 0.03990 ( 633) hydrogen bonds : angle 4.71654 ( 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 147 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6600 (tppt) REVERT: A 234 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7822 (m) REVERT: A 237 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 271 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 440 GLN cc_start: 0.4837 (tt0) cc_final: 0.4172 (tm-30) REVERT: A 460 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.6718 (ttm-80) REVERT: A 732 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5663 (tt0) REVERT: A 767 TYR cc_start: 0.6150 (m-80) cc_final: 0.5823 (m-10) REVERT: A 768 MET cc_start: 0.7324 (mtm) cc_final: 0.6939 (mtm) REVERT: A 779 ILE cc_start: 0.5889 (OUTLIER) cc_final: 0.5417 (tp) REVERT: A 947 ASP cc_start: 0.7123 (m-30) cc_final: 0.6777 (m-30) REVERT: A 959 ARG cc_start: 0.7297 (ttt90) cc_final: 0.6992 (tpt-90) REVERT: A 963 ASN cc_start: 0.7279 (m-40) cc_final: 0.6948 (m-40) REVERT: A 1012 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: A 1145 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7488 (mtp180) REVERT: A 1150 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7707 (mmtm) REVERT: A 1198 ARG cc_start: 0.6986 (tmm160) cc_final: 0.6189 (tpt170) outliers start: 40 outliers final: 14 residues processed: 137 average time/residue: 0.5033 time to fit residues: 76.2764 Evaluate side-chains 122 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 234 SER 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 497 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE 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 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 1372 GLN 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: 0.9990 chunk 76 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4248 r_free = 0.4248 target = 0.203145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156513 restraints weight = 14740.271| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.76 r_work: 0.3513 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1846 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= 0.177 Angle : 0.579 9.225 20341 Z= 0.305 Chirality : 0.040 0.287 2349 Planarity : 0.004 0.048 2138 Dihedral : 20.439 177.094 3399 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 2.87 % Allowed : 15.14 % Favored : 81.99 % 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 aren not related in a simple way. whole: -0.43 (0.22), residues: 1406 helix: 0.39 (0.20), residues: 664 sheet: -0.72 (0.41), residues: 131 loop : -0.85 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.024 0.002 TYR A1117 PHE 0.017 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 covalent geometry : bond 0.00389 (14634) covalent geometry : angle 0.57902 (20341) hydrogen bonds : bond 0.03847 ( 633) hydrogen bonds : angle 4.66702 ( 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 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6649 (tppt) REVERT: A 271 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 326 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8295 (mm110) REVERT: A 460 ARG cc_start: 0.7665 (ttp-170) cc_final: 0.6819 (ttm-80) REVERT: A 732 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5439 (tt0) REVERT: A 767 TYR cc_start: 0.6212 (m-80) cc_final: 0.5859 (m-10) REVERT: A 768 MET cc_start: 0.7455 (mtm) cc_final: 0.7125 (mtm) REVERT: A 773 ASN cc_start: 0.7032 (t0) cc_final: 0.6737 (t160) REVERT: A 779 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5748 (tp) REVERT: A 947 ASP cc_start: 0.7237 (m-30) cc_final: 0.6914 (m-30) REVERT: A 959 ARG cc_start: 0.7497 (ttt90) cc_final: 0.7198 (tpt-90) REVERT: A 963 ASN cc_start: 0.7440 (m-40) cc_final: 0.7138 (m-40) REVERT: A 1012 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 1034 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: A 1133 ASP cc_start: 0.8250 (m-30) cc_final: 0.7727 (t0) REVERT: A 1145 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7578 (mtp180) REVERT: A 1150 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7845 (mmtm) REVERT: A 1198 ARG cc_start: 0.7152 (tmm160) cc_final: 0.6390 (tpt170) outliers start: 36 outliers final: 17 residues processed: 134 average time/residue: 0.5193 time to fit residues: 79.2027 Evaluate side-chains 124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 326 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE 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 1034 ASP 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 1372 GLN 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: 4.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 417 ASN A 928 ASN A 944 HIS A1121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.198222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152234 restraints weight = 14859.442| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.96 r_work: 0.3435 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14634 Z= 0.328 Angle : 0.700 9.683 20341 Z= 0.365 Chirality : 0.046 0.333 2349 Planarity : 0.005 0.056 2138 Dihedral : 20.484 177.032 3399 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.05 % Favored : 93.74 % Rotamer: Outliers : 3.19 % Allowed : 15.78 % Favored : 81.04 % 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 aren not related in a simple way. whole: -0.78 (0.22), residues: 1406 helix: -0.00 (0.20), residues: 665 sheet: -0.76 (0.40), residues: 127 loop : -0.92 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 384 TYR 0.025 0.002 TYR A1117 PHE 0.027 0.002 PHE A1339 TRP 0.012 0.002 TRP A 352 HIS 0.008 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00740 (14634) covalent geometry : angle 0.69980 (20341) hydrogen bonds : bond 0.04735 ( 633) hydrogen bonds : angle 4.97514 ( 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 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6711 (tppt) REVERT: A 237 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: A 271 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 326 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8402 (mm110) REVERT: A 460 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.6934 (ttm-80) REVERT: A 732 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: A 767 TYR cc_start: 0.6394 (m-80) cc_final: 0.6002 (m-10) REVERT: A 768 MET cc_start: 0.7633 (mtm) cc_final: 0.7332 (mtm) REVERT: A 773 ASN cc_start: 0.7207 (t0) cc_final: 0.6972 (t0) REVERT: A 779 ILE cc_start: 0.5976 (OUTLIER) cc_final: 0.5443 (tp) REVERT: A 922 LYS cc_start: 0.7121 (mttm) cc_final: 0.6799 (mttt) REVERT: A 947 ASP cc_start: 0.7507 (m-30) cc_final: 0.7276 (m-30) REVERT: A 959 ARG cc_start: 0.7551 (ttt90) cc_final: 0.7180 (tpt-90) REVERT: A 1012 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: A 1034 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: A 1145 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7615 (mtp180) REVERT: A 1150 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7808 (mmtm) REVERT: A 1198 ARG cc_start: 0.7247 (tmm160) cc_final: 0.6455 (tpt170) outliers start: 40 outliers final: 18 residues processed: 130 average time/residue: 0.5560 time to fit residues: 79.8160 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 : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 326 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1034 ASP 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: 0.9980 chunk 115 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 118 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 632 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 = 0.4242 r_free = 0.4242 target = 0.203740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160574 restraints weight = 14910.704| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.79 r_work: 0.3495 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14634 Z= 0.144 Angle : 0.577 10.583 20341 Z= 0.303 Chirality : 0.039 0.281 2349 Planarity : 0.004 0.049 2138 Dihedral : 20.449 178.821 3399 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 2.47 % Allowed : 16.49 % Favored : 81.04 % 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 aren not related in a simple way. whole: -0.53 (0.22), residues: 1406 helix: 0.33 (0.20), residues: 665 sheet: -0.89 (0.41), residues: 131 loop : -0.90 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 409 TYR 0.026 0.002 TYR A1117 PHE 0.012 0.001 PHE A1339 TRP 0.015 0.001 TRP A 352 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00309 (14634) covalent geometry : angle 0.57724 (20341) hydrogen bonds : bond 0.03779 ( 633) hydrogen bonds : angle 4.66985 ( 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 135 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6752 (tppt) REVERT: A 237 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: A 271 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 326 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: A 732 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: A 767 TYR cc_start: 0.6535 (m-80) cc_final: 0.6188 (m-10) REVERT: A 768 MET cc_start: 0.7779 (mtm) cc_final: 0.7502 (mtm) REVERT: A 779 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5907 (tp) REVERT: A 947 ASP cc_start: 0.7403 (m-30) cc_final: 0.7068 (m-30) REVERT: A 959 ARG cc_start: 0.7786 (ttt90) cc_final: 0.7433 (tpt-90) REVERT: A 1034 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: A 1133 ASP cc_start: 0.8167 (m-30) cc_final: 0.7723 (t0) REVERT: A 1150 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7979 (mmtm) REVERT: A 1198 ARG cc_start: 0.7370 (tmm160) cc_final: 0.6806 (tpt170) outliers start: 31 outliers final: 14 residues processed: 131 average time/residue: 0.5751 time to fit residues: 83.2664 Evaluate side-chains 118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 326 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 732 GLU 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 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 1377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 632 ASN ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4225 r_free = 0.4225 target = 0.201903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157220 restraints weight = 14813.585| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.83 r_work: 0.3466 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14634 Z= 0.192 Angle : 0.603 11.058 20341 Z= 0.316 Chirality : 0.041 0.293 2349 Planarity : 0.004 0.049 2138 Dihedral : 20.409 177.642 3399 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Rotamer: Outliers : 2.47 % Allowed : 16.73 % Favored : 80.80 % 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 aren not related in a simple way. whole: -0.55 (0.22), residues: 1406 helix: 0.30 (0.20), residues: 666 sheet: -0.79 (0.41), residues: 129 loop : -0.91 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.025 0.002 TYR A1117 PHE 0.018 0.002 PHE A1339 TRP 0.015 0.001 TRP A 352 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00423 (14634) covalent geometry : angle 0.60297 (20341) hydrogen bonds : bond 0.03959 ( 633) hydrogen bonds : angle 4.70058 ( 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 130 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6772 (tppt) REVERT: A 237 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: A 271 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 326 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8296 (mm110) REVERT: A 632 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6531 (t0) REVERT: A 683 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7585 (mp) REVERT: A 732 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6181 (tt0) REVERT: A 767 TYR cc_start: 0.6542 (m-80) cc_final: 0.6200 (m-10) REVERT: A 768 MET cc_start: 0.7700 (mtm) cc_final: 0.7434 (mtm) REVERT: A 779 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5864 (tp) REVERT: A 947 ASP cc_start: 0.7437 (m-30) cc_final: 0.7130 (m-30) REVERT: A 1034 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: A 1133 ASP cc_start: 0.8105 (m-30) cc_final: 0.7698 (t0) REVERT: A 1150 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8012 (mmtm) REVERT: A 1198 ARG cc_start: 0.7393 (tmm160) cc_final: 0.6809 (tpt170) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 0.4498 time to fit residues: 63.1349 Evaluate side-chains 119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 326 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 632 ASN Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 1034 ASP 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 1247 THR Chi-restraints excluded: chain A residue 1270 LEU 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: 0.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 632 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 = 0.4232 r_free = 0.4232 target = 0.202677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157970 restraints weight = 14848.809| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.80 r_work: 0.3487 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14634 Z= 0.176 Angle : 0.594 11.204 20341 Z= 0.311 Chirality : 0.040 0.287 2349 Planarity : 0.004 0.048 2138 Dihedral : 20.409 178.070 3399 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.59 % Rotamer: Outliers : 2.39 % Allowed : 16.97 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.22), residues: 1406 helix: 0.33 (0.20), residues: 666 sheet: -0.80 (0.41), residues: 129 loop : -0.92 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.026 0.002 TYR A1117 PHE 0.015 0.001 PHE A1339 TRP 0.015 0.001 TRP A 352 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00387 (14634) covalent geometry : angle 0.59364 (20341) hydrogen bonds : bond 0.03857 ( 633) hydrogen bonds : angle 4.66592 ( 1793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4336.31 seconds wall clock time: 74 minutes 46.59 seconds (4486.59 seconds total)