Starting phenix.real_space_refine on Thu Aug 6 02:28:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wa9_65809/08_2026/9wa9_65809.map" } resolution = 4.12 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 148 5.49 5 S 22 5.16 5 C 7560 2.51 5 N 2272 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1171, 9599 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1141} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1171, 9599 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1141} Chain breaks: 2 bond proxies already assigned to first conformer: 9755 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 37} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 36} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 2131 Classifications: {'RNA': 100} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 40} Link IDs: {'rna2p': 11, 'rna3p': 88} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.72 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.28 Time building chain proxies: 4.09, per 1000 atoms: 0.32 Number of scatterers: 12788 At special positions: 0 Unit cell: (122.436, 114.918, 112.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 148 15.00 O 2786 8.00 N 2272 7.00 C 7560 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: 0.81 Conformation dependent library (CDL) restraints added in 743.4 milliseconds 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 56.3% alpha, 7.5% beta 56 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.194A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.716A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.504A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.771A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.537A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.512A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.223A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.802A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.618A pdb=" N VAL A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 495 removed outlier: 4.416A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.862A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.891A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 752 removed outlier: 3.712A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 778 removed outlier: 3.574A pdb=" N GLY A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 802 through 808 removed outlier: 3.784A pdb=" N ASN A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.513A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 818 " --> pdb=" O TYR A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 836 removed outlier: 4.238A pdb=" N ASP A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.788A pdb=" N LYS A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 890 removed outlier: 4.935A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 removed outlier: 4.477A pdb=" N ALA A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU A 904 " --> pdb=" O LEU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.798A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 3.800A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.057A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 removed outlier: 3.502A pdb=" N ILE A 998 " --> pdb=" O GLY A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.518A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 removed outlier: 3.529A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 955 removed outlier: 4.049A pdb=" N ILE A 759 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.536A pdb=" N ILE A 43 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.679A pdb=" N HIS A1349 " --> pdb=" O THR A1358 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A1348 " --> pdb=" O LEU A1203 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A1219 " --> pdb=" O SER A1216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 560 removed outlier: 4.683A pdb=" N VAL A 559 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA7, first strand: chain 'A' and resid 1139 through 1151 removed outlier: 3.518A pdb=" N VAL A1143 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.898A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.07 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: 2670 1.33 - 1.45: 3618 1.45 - 1.57: 6713 1.57 - 1.69: 296 1.69 - 1.81: 42 Bond restraints: 13339 Sorted by residual: bond pdb=" C3' DC B 13 " pdb=" C2' DC B 13 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.67e+00 bond pdb=" C3' DT B 17 " pdb=" C2' DT B 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 bond pdb=" C3' DT B 10 " pdb=" C2' DT B 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.07e+00 bond pdb=" C3' DA B 39 " pdb=" C2' DA B 39 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 ... (remaining 13334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 17947 1.72 - 3.45: 666 3.45 - 5.17: 31 5.17 - 6.89: 9 6.89 - 8.62: 3 Bond angle restraints: 18656 Sorted by residual: angle pdb=" O4' DA B 22 " pdb=" C4' DA B 22 " pdb=" C3' DA B 22 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" O4' DC B 29 " pdb=" C4' DC B 29 " pdb=" C3' DC B 29 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT B 33 " pdb=" C4 DT B 33 " pdb=" O4 DT B 33 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" O4' DG B 32 " pdb=" C4' DG B 32 " pdb=" C3' DG B 32 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 18651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6997 17.77 - 35.55: 691 35.55 - 53.32: 230 53.32 - 71.10: 137 71.10 - 88.87: 37 Dihedral angle restraints: 8092 sinusoidal: 4648 harmonic: 3444 Sorted by residual: dihedral pdb=" CA ILE A 759 " pdb=" C ILE A 759 " pdb=" N VAL A 760 " pdb=" CA VAL A 760 " ideal model delta harmonic sigma weight residual 180.00 123.94 56.06 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA VAL A 760 " pdb=" C VAL A 760 " pdb=" N ILE A 761 " pdb=" CA ILE A 761 " ideal model delta harmonic sigma weight residual -180.00 -147.17 -32.83 0 5.00e+00 4.00e-02 4.31e+01 dihedral pdb=" CA ARG A 765 " pdb=" C ARG A 765 " pdb=" N GLU A 766 " pdb=" CA GLU A 766 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 8089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1832 0.063 - 0.127: 227 0.127 - 0.190: 81 0.190 - 0.254: 0 0.254 - 0.317: 1 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CB VAL A 760 " pdb=" CA VAL A 760 " pdb=" CG1 VAL A 760 " pdb=" CG2 VAL A 760 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C1' A D 36 " pdb=" O4' A D 36 " pdb=" C2' A D 36 " pdb=" N9 A D 36 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" C2' A D 7 " pdb=" C3' A D 7 " pdb=" O2' A D 7 " pdb=" C1' A D 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2138 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 759 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ILE A 759 " 0.046 2.00e-02 2.50e+03 pdb=" O ILE A 759 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 760 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 755 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 756 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 756 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 756 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 36 " 0.023 2.00e-02 2.50e+03 1.09e-02 3.25e+00 pdb=" N9 A D 36 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A D 36 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 36 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A D 36 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A D 36 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D 36 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 36 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 36 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 8 2.02 - 2.74: 1089 2.74 - 3.46: 18638 3.46 - 4.18: 32940 4.18 - 4.90: 51859 Nonbonded interactions: 104534 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG A1333 " pdb=" O6 DG C 3 " model vdw 1.298 3.120 nonbonded pdb=" NE2 GLN A1221 " pdb=" OP1 DG C 3 " model vdw 1.298 3.120 nonbonded pdb=" NH1 ARG A1335 " pdb=" O6 DG C 4 " model vdw 1.299 3.120 nonbonded pdb=" NZ LYS A1340 " pdb=" OP2 DA B 8 " model vdw 1.300 3.120 ... (remaining 104529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 0.038 13339 Z= 0.254 Angle : 0.663 8.616 18656 Z= 0.487 Chirality : 0.047 0.317 2141 Planarity : 0.004 0.057 1834 Dihedral : 17.572 88.873 5864 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 0.09 % Allowed : 0.38 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1168 helix: 1.04 (0.22), residues: 585 sheet: -0.00 (0.67), residues: 54 loop : -0.43 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 71 TYR 0.012 0.001 TYR A 594 PHE 0.016 0.001 PHE A 86 TRP 0.008 0.001 TRP A1126 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.25 (13339) covalent geometry : angle 0.66335 / 0.49 (18656) hydrogen bonds : bond 0.15504 / 10.51 ( 585) hydrogen bonds : angle 5.94761 / 4.21 ( 1568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.9031 (tp) cc_final: 0.8553 (tt) REVERT: A 399 LEU cc_start: 0.8303 (mt) cc_final: 0.7871 (mt) REVERT: A 703 THR cc_start: 0.8046 (p) cc_final: 0.7161 (p) REVERT: A 707 ASP cc_start: 0.9383 (m-30) cc_final: 0.9098 (m-30) REVERT: A 1350 GLN cc_start: 0.8425 (mm110) cc_final: 0.8073 (mm110) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1192 time to fit residues: 29.3252 Evaluate side-chains 98 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 10.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 GLN A 863 ASN A 980 ASN A 990 ASN A1256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.058590 restraints weight = 252018.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.060803 restraints weight = 113064.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.062251 restraints weight = 67302.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.063158 restraints weight = 46971.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063757 restraints weight = 36469.936| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13339 Z= 0.183 Angle : 0.651 9.123 18656 Z= 0.370 Chirality : 0.043 0.258 2141 Planarity : 0.008 0.225 1834 Dihedral : 18.515 77.085 3349 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 0.19 % Allowed : 1.52 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1168 helix: 0.78 (0.21), residues: 605 sheet: -0.12 (0.61), residues: 61 loop : -0.76 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 71 TYR 0.016 0.002 TYR A 836 PHE 0.019 0.002 PHE A 372 TRP 0.008 0.001 TRP A1126 HIS 0.008 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (13339) covalent geometry : angle 0.65135 / 0.37 (18656) hydrogen bonds : bond 0.06467 / 4.23 ( 585) hydrogen bonds : angle 4.94346 / 3.42 ( 1568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5860 (ptm) cc_final: 0.5415 (ppp) REVERT: A 631 MET cc_start: 0.9497 (mmp) cc_final: 0.9266 (mmm) REVERT: A 707 ASP cc_start: 0.9557 (m-30) cc_final: 0.9264 (m-30) REVERT: A 936 ASP cc_start: 0.9549 (m-30) cc_final: 0.9281 (m-30) REVERT: A 943 TYR cc_start: 0.8814 (m-80) cc_final: 0.8540 (m-80) REVERT: A 981 TYR cc_start: 0.8564 (m-80) cc_final: 0.8069 (m-80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1250 time to fit residues: 20.3329 Evaluate side-chains 80 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 17 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.067087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.055891 restraints weight = 165786.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.057599 restraints weight = 87617.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.058686 restraints weight = 57007.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.059392 restraints weight = 42436.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.059828 restraints weight = 34379.230| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13339 Z= 0.232 Angle : 0.659 15.067 18656 Z= 0.375 Chirality : 0.042 0.251 2141 Planarity : 0.007 0.180 1834 Dihedral : 18.570 76.087 3349 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.28 % Allowed : 1.52 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1168 helix: 0.53 (0.21), residues: 613 sheet: 0.01 (0.62), residues: 66 loop : -0.93 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 324 TYR 0.015 0.002 TYR A 132 PHE 0.031 0.002 PHE A1276 TRP 0.011 0.001 TRP A 659 HIS 0.010 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 (13339) covalent geometry : angle 0.65923 / 0.38 (18656) hydrogen bonds : bond 0.06468 / 4.27 ( 585) hydrogen bonds : angle 4.87219 / 3.34 ( 1568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.9467 (mmp) cc_final: 0.9255 (mmp) REVERT: A 495 MET cc_start: 0.9577 (mpp) cc_final: 0.9231 (mpp) REVERT: A 534 MET cc_start: 0.5753 (ptm) cc_final: 0.5395 (ppp) REVERT: A 631 MET cc_start: 0.9487 (mmp) cc_final: 0.9220 (mmm) REVERT: A 707 ASP cc_start: 0.9587 (m-30) cc_final: 0.9285 (m-30) REVERT: A 739 GLN cc_start: 0.9710 (mm-40) cc_final: 0.9297 (mm-40) REVERT: A 928 THR cc_start: 0.9020 (p) cc_final: 0.8668 (p) REVERT: A 943 TYR cc_start: 0.8756 (m-80) cc_final: 0.8528 (m-80) REVERT: A 981 TYR cc_start: 0.8701 (m-80) cc_final: 0.8063 (m-80) REVERT: A 1089 MET cc_start: 0.9068 (mpp) cc_final: 0.8744 (mpp) REVERT: A 1097 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8718 (tmtt) REVERT: A 1201 TYR cc_start: 0.9277 (m-80) cc_final: 0.8933 (m-80) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1198 time to fit residues: 18.3900 Evaluate side-chains 74 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 40.0000 chunk 47 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.064257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052999 restraints weight = 191713.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.054753 restraints weight = 96536.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055894 restraints weight = 62086.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.056634 restraints weight = 45608.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.057127 restraints weight = 36609.881| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13339 Z= 0.244 Angle : 0.667 8.135 18656 Z= 0.379 Chirality : 0.043 0.297 2141 Planarity : 0.006 0.125 1834 Dihedral : 18.743 77.464 3349 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.19 % Allowed : 1.42 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1168 helix: 0.34 (0.20), residues: 613 sheet: 0.39 (0.78), residues: 44 loop : -0.91 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 63 TYR 0.014 0.002 TYR A 132 PHE 0.022 0.002 PHE A 972 TRP 0.034 0.003 TRP A1126 HIS 0.010 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.24 (13339) covalent geometry : angle 0.66720 / 0.38 (18656) hydrogen bonds : bond 0.06432 / 4.30 ( 585) hydrogen bonds : angle 4.88232 / 3.36 ( 1568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.9420 (mmp) cc_final: 0.9126 (mmp) REVERT: A 495 MET cc_start: 0.9546 (mpp) cc_final: 0.9193 (mpp) REVERT: A 534 MET cc_start: 0.5388 (ptm) cc_final: 0.5058 (ppp) REVERT: A 631 MET cc_start: 0.9430 (mmp) cc_final: 0.9136 (mmm) REVERT: A 707 ASP cc_start: 0.9649 (m-30) cc_final: 0.9398 (m-30) REVERT: A 739 GLN cc_start: 0.9725 (mm-40) cc_final: 0.9314 (mm-40) REVERT: A 939 MET cc_start: 0.7959 (tmm) cc_final: 0.7749 (tmm) REVERT: A 943 TYR cc_start: 0.8791 (m-80) cc_final: 0.8537 (m-80) REVERT: A 981 TYR cc_start: 0.8920 (m-10) cc_final: 0.8644 (m-80) REVERT: A 1097 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8709 (tmtt) REVERT: A 1201 TYR cc_start: 0.9381 (m-80) cc_final: 0.8945 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1091 time to fit residues: 15.1671 Evaluate side-chains 67 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 869 ASN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.061995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.051203 restraints weight = 180297.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052864 restraints weight = 93176.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053915 restraints weight = 60543.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.054604 restraints weight = 44873.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.055059 restraints weight = 36370.976| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13339 Z= 0.226 Angle : 0.676 12.411 18656 Z= 0.381 Chirality : 0.043 0.250 2141 Planarity : 0.006 0.082 1834 Dihedral : 18.885 79.464 3349 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.19 % Allowed : 2.27 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1168 helix: 0.16 (0.20), residues: 612 sheet: 0.17 (0.78), residues: 44 loop : -1.03 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 655 TYR 0.019 0.002 TYR A1294 PHE 0.024 0.002 PHE A 626 TRP 0.019 0.002 TRP A1126 HIS 0.014 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.23 (13339) covalent geometry : angle 0.67550 / 0.38 (18656) hydrogen bonds : bond 0.06078 / 4.01 ( 585) hydrogen bonds : angle 4.87931 / 3.36 ( 1568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.9383 (mmp) cc_final: 0.9024 (mmp) REVERT: A 495 MET cc_start: 0.9486 (mpp) cc_final: 0.9074 (mpp) REVERT: A 534 MET cc_start: 0.6038 (ptm) cc_final: 0.5591 (ppp) REVERT: A 631 MET cc_start: 0.9418 (mmp) cc_final: 0.9112 (mmm) REVERT: A 707 ASP cc_start: 0.9711 (m-30) cc_final: 0.9489 (m-30) REVERT: A 739 GLN cc_start: 0.9723 (mm-40) cc_final: 0.9320 (mm-40) REVERT: A 812 TYR cc_start: 0.9234 (t80) cc_final: 0.9014 (t80) REVERT: A 879 MET cc_start: 0.8858 (tpp) cc_final: 0.8312 (tpp) REVERT: A 939 MET cc_start: 0.8115 (tmm) cc_final: 0.7740 (tmm) REVERT: A 943 TYR cc_start: 0.8837 (m-80) cc_final: 0.8584 (m-80) REVERT: A 981 TYR cc_start: 0.8980 (m-10) cc_final: 0.8728 (m-80) REVERT: A 1169 MET cc_start: 0.7326 (tpt) cc_final: 0.7094 (tpt) REVERT: A 1201 TYR cc_start: 0.9426 (m-80) cc_final: 0.8976 (m-80) REVERT: A 1204 PHE cc_start: 0.9328 (m-10) cc_final: 0.8964 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1098 time to fit residues: 14.3285 Evaluate side-chains 65 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051818 restraints weight = 183561.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053536 restraints weight = 93704.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054621 restraints weight = 59946.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.055327 restraints weight = 44156.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.055736 restraints weight = 35497.444| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13339 Z= 0.167 Angle : 0.592 6.766 18656 Z= 0.343 Chirality : 0.041 0.244 2141 Planarity : 0.005 0.078 1834 Dihedral : 18.854 80.494 3349 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 0.19 % Allowed : 0.47 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1168 helix: 0.42 (0.21), residues: 606 sheet: 0.24 (0.78), residues: 44 loop : -0.86 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 629 TYR 0.015 0.002 TYR A1294 PHE 0.016 0.002 PHE A 970 TRP 0.016 0.002 TRP A1126 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (13339) covalent geometry : angle 0.59244 / 0.34 (18656) hydrogen bonds : bond 0.05523 / 3.60 ( 585) hydrogen bonds : angle 4.70570 / 3.25 ( 1568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.9338 (mmp) cc_final: 0.9004 (mmp) REVERT: A 495 MET cc_start: 0.9476 (mpp) cc_final: 0.9059 (mpp) REVERT: A 534 MET cc_start: 0.6205 (ptm) cc_final: 0.5817 (ppp) REVERT: A 564 LEU cc_start: 0.9341 (mm) cc_final: 0.8730 (mm) REVERT: A 587 PHE cc_start: 0.8262 (m-80) cc_final: 0.7876 (m-80) REVERT: A 631 MET cc_start: 0.9343 (mmp) cc_final: 0.9028 (mmm) REVERT: A 707 ASP cc_start: 0.9719 (m-30) cc_final: 0.9490 (m-30) REVERT: A 739 GLN cc_start: 0.9720 (mm-40) cc_final: 0.9345 (mm-40) REVERT: A 812 TYR cc_start: 0.9224 (t80) cc_final: 0.8994 (t80) REVERT: A 939 MET cc_start: 0.8129 (tmm) cc_final: 0.7694 (tmm) REVERT: A 943 TYR cc_start: 0.8869 (m-80) cc_final: 0.8621 (m-80) REVERT: A 981 TYR cc_start: 0.8950 (m-10) cc_final: 0.8697 (m-80) REVERT: A 1169 MET cc_start: 0.7277 (tpt) cc_final: 0.6889 (tpt) REVERT: A 1201 TYR cc_start: 0.9430 (m-80) cc_final: 0.9003 (m-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1150 time to fit residues: 15.0650 Evaluate side-chains 64 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 123 optimal weight: 40.0000 chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 overall best weight: 5.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.034271 restraints weight = 196935.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035814 restraints weight = 109251.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.036852 restraints weight = 75401.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037443 restraints weight = 58319.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.037975 restraints weight = 49475.109| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13339 Z= 0.181 Angle : 0.595 7.710 18656 Z= 0.342 Chirality : 0.041 0.416 2141 Planarity : 0.005 0.064 1834 Dihedral : 18.845 80.821 3349 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer: Outliers : 0.19 % Allowed : 0.47 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1168 helix: 0.30 (0.21), residues: 608 sheet: -0.69 (0.69), residues: 59 loop : -0.85 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1171 TYR 0.016 0.002 TYR A1294 PHE 0.019 0.002 PHE A 972 TRP 0.016 0.002 TRP A1126 HIS 0.011 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (13339) covalent geometry : angle 0.59501 / 0.34 (18656) hydrogen bonds : bond 0.05542 / 3.60 ( 585) hydrogen bonds : angle 4.64915 / 3.22 ( 1568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9432 (mtp) cc_final: 0.9035 (mtp) REVERT: A 321 MET cc_start: 0.9341 (mmp) cc_final: 0.8960 (mmp) REVERT: A 495 MET cc_start: 0.9559 (mpp) cc_final: 0.9067 (mpp) REVERT: A 564 LEU cc_start: 0.9352 (mm) cc_final: 0.9024 (mm) REVERT: A 629 ARG cc_start: 0.9613 (ppt170) cc_final: 0.9409 (ptm-80) REVERT: A 739 GLN cc_start: 0.9679 (mm-40) cc_final: 0.9341 (mm-40) REVERT: A 812 TYR cc_start: 0.9249 (t80) cc_final: 0.9010 (t80) REVERT: A 939 MET cc_start: 0.8274 (tmm) cc_final: 0.7860 (tmm) REVERT: A 943 TYR cc_start: 0.8912 (m-80) cc_final: 0.8701 (m-80) REVERT: A 981 TYR cc_start: 0.9069 (m-10) cc_final: 0.8817 (m-80) REVERT: A 1169 MET cc_start: 0.7797 (tpt) cc_final: 0.7386 (tpt) REVERT: A 1201 TYR cc_start: 0.9519 (m-80) cc_final: 0.9056 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1123 time to fit residues: 14.4348 Evaluate side-chains 63 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 2 optimal weight: 0.5980 chunk 128 optimal weight: 50.0000 chunk 98 optimal weight: 8.9990 overall best weight: 4.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.048202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034200 restraints weight = 222395.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035881 restraints weight = 117671.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.037009 restraints weight = 78733.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.037690 restraints weight = 60091.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038254 restraints weight = 50237.899| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13339 Z= 0.154 Angle : 0.565 9.389 18656 Z= 0.330 Chirality : 0.040 0.302 2141 Planarity : 0.005 0.062 1834 Dihedral : 18.836 81.338 3349 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1168 helix: 0.46 (0.21), residues: 601 sheet: -0.67 (0.68), residues: 59 loop : -0.73 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 63 TYR 0.014 0.002 TYR A 521 PHE 0.014 0.002 PHE A1204 TRP 0.013 0.002 TRP A1126 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (13339) covalent geometry : angle 0.56500 / 0.33 (18656) hydrogen bonds : bond 0.05268 / 3.38 ( 585) hydrogen bonds : angle 4.57426 / 3.14 ( 1568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9372 (mtp) cc_final: 0.8957 (mtp) REVERT: A 321 MET cc_start: 0.9294 (mmp) cc_final: 0.8918 (mmp) REVERT: A 495 MET cc_start: 0.9558 (mpp) cc_final: 0.9071 (mpp) REVERT: A 521 TYR cc_start: 0.9129 (m-80) cc_final: 0.8815 (m-80) REVERT: A 587 PHE cc_start: 0.7981 (m-80) cc_final: 0.7383 (m-80) REVERT: A 629 ARG cc_start: 0.9608 (ppt170) cc_final: 0.9362 (ptm-80) REVERT: A 631 MET cc_start: 0.9350 (mmp) cc_final: 0.9122 (mmm) REVERT: A 739 GLN cc_start: 0.9682 (mm-40) cc_final: 0.9333 (mm-40) REVERT: A 939 MET cc_start: 0.8269 (tmm) cc_final: 0.7917 (tmm) REVERT: A 943 TYR cc_start: 0.8943 (m-80) cc_final: 0.8734 (m-80) REVERT: A 981 TYR cc_start: 0.9070 (m-10) cc_final: 0.8825 (m-80) REVERT: A 1089 MET cc_start: 0.8781 (mpp) cc_final: 0.8471 (mpp) REVERT: A 1169 MET cc_start: 0.7829 (tpt) cc_final: 0.7455 (tpt) REVERT: A 1201 TYR cc_start: 0.9500 (m-80) cc_final: 0.8982 (m-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1111 time to fit residues: 14.7772 Evaluate side-chains 64 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 0.0170 chunk 119 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 123 optimal weight: 50.0000 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.048991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034770 restraints weight = 221365.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.036455 restraints weight = 116194.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.037639 restraints weight = 78134.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.038373 restraints weight = 59232.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.038937 restraints weight = 49190.397| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13339 Z= 0.123 Angle : 0.531 6.863 18656 Z= 0.311 Chirality : 0.039 0.313 2141 Planarity : 0.004 0.049 1834 Dihedral : 18.766 81.715 3349 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 0.19 % Allowed : 0.28 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1168 helix: 0.60 (0.21), residues: 602 sheet: -0.82 (0.56), residues: 81 loop : -0.65 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 780 TYR 0.011 0.001 TYR A 155 PHE 0.012 0.001 PHE A 970 TRP 0.015 0.001 TRP A1126 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (13339) covalent geometry : angle 0.53143 / 0.31 (18656) hydrogen bonds : bond 0.04991 / 3.15 ( 585) hydrogen bonds : angle 4.41317 / 3.05 ( 1568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8363 (tpp) cc_final: 0.8123 (tpp) REVERT: A 161 MET cc_start: 0.9386 (mtp) cc_final: 0.8950 (mtp) REVERT: A 321 MET cc_start: 0.9268 (mmp) cc_final: 0.8909 (mmp) REVERT: A 495 MET cc_start: 0.9571 (mpp) cc_final: 0.9126 (mpp) REVERT: A 521 TYR cc_start: 0.9111 (m-80) cc_final: 0.8800 (m-80) REVERT: A 587 PHE cc_start: 0.8019 (m-80) cc_final: 0.7485 (m-80) REVERT: A 629 ARG cc_start: 0.9598 (ppt170) cc_final: 0.9350 (ptm-80) REVERT: A 631 MET cc_start: 0.9310 (mmp) cc_final: 0.9095 (mmm) REVERT: A 707 ASP cc_start: 0.9603 (m-30) cc_final: 0.9394 (m-30) REVERT: A 739 GLN cc_start: 0.9677 (mm-40) cc_final: 0.9326 (mm-40) REVERT: A 879 MET cc_start: 0.8813 (tpp) cc_final: 0.8602 (tpp) REVERT: A 928 THR cc_start: 0.9310 (m) cc_final: 0.8970 (m) REVERT: A 943 TYR cc_start: 0.8950 (m-80) cc_final: 0.8674 (m-80) REVERT: A 981 TYR cc_start: 0.9052 (m-10) cc_final: 0.8832 (m-80) REVERT: A 1169 MET cc_start: 0.7787 (tpt) cc_final: 0.7458 (tpt) REVERT: A 1201 TYR cc_start: 0.9456 (m-80) cc_final: 0.8941 (m-80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1138 time to fit residues: 15.5213 Evaluate side-chains 69 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.0470 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034322 restraints weight = 204136.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035923 restraints weight = 112127.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037006 restraints weight = 76513.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.037665 restraints weight = 58860.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.038189 restraints weight = 49482.158| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13339 Z= 0.155 Angle : 0.546 6.890 18656 Z= 0.319 Chirality : 0.038 0.278 2141 Planarity : 0.004 0.058 1834 Dihedral : 18.770 80.798 3349 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1168 helix: 0.58 (0.21), residues: 604 sheet: -0.80 (0.57), residues: 81 loop : -0.62 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 63 TYR 0.012 0.001 TYR A1294 PHE 0.012 0.001 PHE A 626 TRP 0.013 0.002 TRP A1126 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (13339) covalent geometry : angle 0.54567 / 0.32 (18656) hydrogen bonds : bond 0.05185 / 3.32 ( 585) hydrogen bonds : angle 4.46581 / 3.09 ( 1568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2336 Ramachandran restraints generated. 1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9365 (mtp) cc_final: 0.8960 (mtp) REVERT: A 321 MET cc_start: 0.9271 (mmp) cc_final: 0.8874 (mmp) REVERT: A 495 MET cc_start: 0.9558 (mpp) cc_final: 0.9130 (mpp) REVERT: A 521 TYR cc_start: 0.9105 (m-80) cc_final: 0.8793 (m-80) REVERT: A 629 ARG cc_start: 0.9595 (ppt170) cc_final: 0.9374 (ptm-80) REVERT: A 631 MET cc_start: 0.9322 (mmp) cc_final: 0.9093 (mmm) REVERT: A 707 ASP cc_start: 0.9580 (m-30) cc_final: 0.9364 (m-30) REVERT: A 739 GLN cc_start: 0.9680 (mm-40) cc_final: 0.9346 (mm-40) REVERT: A 879 MET cc_start: 0.8735 (tpp) cc_final: 0.8524 (tpp) REVERT: A 943 TYR cc_start: 0.8966 (m-80) cc_final: 0.8673 (m-80) REVERT: A 981 TYR cc_start: 0.9075 (m-10) cc_final: 0.8837 (m-80) REVERT: A 1169 MET cc_start: 0.7933 (tpt) cc_final: 0.7620 (tpt) REVERT: A 1201 TYR cc_start: 0.9461 (m-80) cc_final: 0.8957 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1093 time to fit residues: 13.8774 Evaluate side-chains 65 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 129 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 84 optimal weight: 0.1980 chunk 28 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.049385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035378 restraints weight = 189376.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.036972 restraints weight = 105516.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.038083 restraints weight = 72448.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.038762 restraints weight = 55724.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.039323 restraints weight = 46798.818| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13339 Z= 0.116 Angle : 0.519 6.795 18656 Z= 0.303 Chirality : 0.038 0.305 2141 Planarity : 0.004 0.049 1834 Dihedral : 18.721 81.796 3349 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1168 helix: 0.73 (0.22), residues: 605 sheet: -0.62 (0.57), residues: 81 loop : -0.56 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 780 TYR 0.010 0.001 TYR A1141 PHE 0.012 0.001 PHE A1080 TRP 0.014 0.001 TRP A1126 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.12 (13339) covalent geometry : angle 0.51906 / 0.30 (18656) hydrogen bonds : bond 0.04890 / 3.08 ( 585) hydrogen bonds : angle 4.31972 / 2.99 ( 1568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.92 seconds wall clock time: 43 minutes 17.05 seconds (2597.05 seconds total)