Starting phenix.real_space_refine on Fri Jul 3 08:07:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wa9_65809/07_2026/9wa9_65809.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wa9_65809/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9wa9_65809/07_2026/9wa9_65809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wa9_65809/07_2026/9wa9_65809.map" model { file = "/net/cci-nas-00/data/ceres_data/9wa9_65809/07_2026/9wa9_65809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wa9_65809/07_2026/9wa9_65809.cif" } 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-dev-6108/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: 4.18, per 1000 atoms: 0.33 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: 1.20 Conformation dependent library (CDL) restraints added in 840.7 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: 3.45 Time building geometry restraints manager: 1.60 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: 18217 1.72 - 3.45: 396 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: 1938 0.063 - 0.127: 195 0.127 - 0.190: 7 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 2.46 2.29 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA GLU A 779 " pdb=" N GLU A 779 " pdb=" C GLU A 779 " pdb=" CB GLU A 779 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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= 0.249 Angle : 0.595 8.616 18656 Z= 0.431 Chirality : 0.038 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 0.00313 / 0.25 (13339) covalent geometry : angle 0.59530 / 0.43 (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 : 0.458 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: 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: 0.7877 (mt) REVERT: A 703 THR cc_start: 0.8046 (p) cc_final: 0.7163 (p) REVERT: A 707 ASP cc_start: 0.9383 (m-30) cc_final: 0.9100 (m-30) REVERT: A 1350 GLN cc_start: 0.8425 (mm110) cc_final: 0.8075 (mm110) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1458 time to fit residues: 35.4718 Evaluate side-chains 100 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.071394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.058787 restraints weight = 254787.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.061099 restraints weight = 113118.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.062540 restraints weight = 67457.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.063457 restraints weight = 47144.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.064090 restraints weight = 36371.771| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13339 Z= 0.183 Angle : 0.626 9.801 18656 Z= 0.359 Chirality : 0.042 0.258 2141 Planarity : 0.006 0.078 1834 Dihedral : 18.570 76.863 3349 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.78 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: 0.11 (0.24), residues: 1168 helix: 0.81 (0.21), residues: 606 sheet: -0.11 (0.61), residues: 61 loop : -0.75 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1171 TYR 0.023 0.002 TYR A 836 PHE 0.020 0.002 PHE A 86 TRP 0.008 0.001 TRP A1126 HIS 0.007 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (13339) covalent geometry : angle 0.62616 / 0.36 (18656) hydrogen bonds : bond 0.06579 / 4.30 ( 585) hydrogen bonds : angle 4.95125 / 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 114 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.307 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: A 534 MET cc_start: 0.5890 (ptm) cc_final: 0.5425 (ppp) REVERT: A 631 MET cc_start: 0.9494 (mmp) cc_final: 0.9279 (mmm) REVERT: A 707 ASP cc_start: 0.9556 (m-30) cc_final: 0.9262 (m-30) REVERT: A 936 ASP cc_start: 0.9539 (m-30) cc_final: 0.9266 (m-30) REVERT: A 943 TYR cc_start: 0.8809 (m-80) cc_final: 0.8536 (m-80) REVERT: A 981 TYR cc_start: 0.8534 (m-80) cc_final: 0.8038 (m-80) REVERT: A 1201 TYR cc_start: 0.9257 (m-80) cc_final: 0.9039 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1299 time to fit residues: 20.5620 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 : 0.267 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 117 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 863 ASN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.069945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.058696 restraints weight = 162200.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.060349 restraints weight = 84664.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.061477 restraints weight = 55182.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.062212 restraints weight = 40716.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.062715 restraints weight = 32758.271| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13339 Z= 0.165 Angle : 0.588 14.007 18656 Z= 0.339 Chirality : 0.040 0.284 2141 Planarity : 0.005 0.046 1834 Dihedral : 18.554 77.235 3349 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 0.19 % Allowed : 1.33 % Favored : 98.48 % 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: 0.06 (0.24), residues: 1168 helix: 0.76 (0.21), residues: 607 sheet: 0.09 (0.61), residues: 66 loop : -0.80 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 307 TYR 0.012 0.001 TYR A1141 PHE 0.030 0.002 PHE A1276 TRP 0.006 0.001 TRP A 659 HIS 0.008 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (13339) covalent geometry : angle 0.58783 / 0.34 (18656) hydrogen bonds : bond 0.05852 / 3.78 ( 585) hydrogen bonds : angle 4.71661 / 3.24 ( 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 103 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.358 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 75 ARG cc_start: 0.9660 (ttm170) cc_final: 0.9446 (ptm-80) REVERT: A 495 MET cc_start: 0.9591 (mpp) cc_final: 0.9236 (mpp) REVERT: A 534 MET cc_start: 0.5569 (ptm) cc_final: 0.5118 (ppp) REVERT: A 631 MET cc_start: 0.9497 (mmp) cc_final: 0.9250 (mmm) REVERT: A 707 ASP cc_start: 0.9551 (m-30) cc_final: 0.9256 (m-30) REVERT: A 739 GLN cc_start: 0.9682 (mm-40) cc_final: 0.9280 (mm-40) REVERT: A 879 MET cc_start: 0.8145 (tpt) cc_final: 0.7657 (tpp) REVERT: A 928 THR cc_start: 0.8943 (p) cc_final: 0.8609 (p) REVERT: A 943 TYR cc_start: 0.8776 (m-80) cc_final: 0.8530 (m-80) REVERT: A 981 TYR cc_start: 0.8676 (m-80) cc_final: 0.8142 (m-80) REVERT: A 1089 MET cc_start: 0.9014 (mpp) cc_final: 0.8720 (mpp) REVERT: A 1201 TYR cc_start: 0.9307 (m-80) cc_final: 0.9081 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1160 time to fit residues: 17.1346 Evaluate side-chains 78 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.067528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.056014 restraints weight = 186249.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.057916 restraints weight = 93541.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.059077 restraints weight = 59159.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.059842 restraints weight = 43183.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.060359 restraints weight = 34439.222| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13339 Z= 0.188 Angle : 0.596 8.665 18656 Z= 0.344 Chirality : 0.040 0.205 2141 Planarity : 0.005 0.056 1834 Dihedral : 18.615 78.440 3349 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 0.19 % Allowed : 1.33 % Favored : 98.48 % 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: -0.06 (0.24), residues: 1168 helix: 0.65 (0.21), residues: 612 sheet: 0.06 (0.62), residues: 66 loop : -0.86 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 629 TYR 0.016 0.002 TYR A 5 PHE 0.016 0.002 PHE A1204 TRP 0.049 0.004 TRP A1126 HIS 0.011 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 (13339) covalent geometry : angle 0.59559 / 0.34 (18656) hydrogen bonds : bond 0.05773 / 3.77 ( 585) hydrogen bonds : angle 4.62290 / 3.18 ( 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 98 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.449 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 321 MET cc_start: 0.9349 (mmp) cc_final: 0.9145 (mmp) REVERT: A 495 MET cc_start: 0.9580 (mpp) cc_final: 0.9220 (mpp) REVERT: A 534 MET cc_start: 0.5441 (ptm) cc_final: 0.5080 (ppp) REVERT: A 631 MET cc_start: 0.9416 (mmp) cc_final: 0.9110 (mmm) REVERT: A 707 ASP cc_start: 0.9610 (m-30) cc_final: 0.9328 (m-30) REVERT: A 739 GLN cc_start: 0.9709 (mm-40) cc_final: 0.9287 (mm-40) REVERT: A 812 TYR cc_start: 0.9163 (t80) cc_final: 0.8945 (t80) REVERT: A 936 ASP cc_start: 0.9322 (m-30) cc_final: 0.9026 (m-30) REVERT: A 943 TYR cc_start: 0.8763 (m-80) cc_final: 0.8472 (m-80) REVERT: A 981 TYR cc_start: 0.8835 (m-10) cc_final: 0.8579 (m-80) REVERT: A 1097 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8755 (tmtt) REVERT: A 1201 TYR cc_start: 0.9362 (m-80) cc_final: 0.9060 (m-80) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1157 time to fit residues: 16.4946 Evaluate side-chains 72 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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: 0.6980 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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** A 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.066502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055349 restraints weight = 175137.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.057093 restraints weight = 90035.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.058224 restraints weight = 57807.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.058947 restraints weight = 42432.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.059446 restraints weight = 34042.251| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13339 Z= 0.169 Angle : 0.579 8.278 18656 Z= 0.335 Chirality : 0.040 0.321 2141 Planarity : 0.005 0.122 1834 Dihedral : 18.659 79.947 3349 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % 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: -0.07 (0.24), residues: 1168 helix: 0.68 (0.21), residues: 612 sheet: -0.66 (0.56), residues: 76 loop : -0.80 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 655 TYR 0.012 0.002 TYR A 943 PHE 0.015 0.002 PHE A1276 TRP 0.020 0.001 TRP A1126 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (13339) covalent geometry : angle 0.57896 / 0.33 (18656) hydrogen bonds : bond 0.05466 / 3.55 ( 585) hydrogen bonds : angle 4.52661 / 3.11 ( 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 95 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.422 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 86 PHE cc_start: 0.9497 (m-80) cc_final: 0.9291 (m-80) REVERT: A 321 MET cc_start: 0.9326 (mmp) cc_final: 0.9096 (mmp) REVERT: A 495 MET cc_start: 0.9552 (mpp) cc_final: 0.9180 (mpp) REVERT: A 534 MET cc_start: 0.5339 (ptm) cc_final: 0.4995 (ppp) REVERT: A 629 ARG cc_start: 0.9548 (ppt170) cc_final: 0.9336 (ptm-80) REVERT: A 631 MET cc_start: 0.9380 (mmp) cc_final: 0.9103 (mmm) REVERT: A 707 ASP cc_start: 0.9618 (m-30) cc_final: 0.9362 (m-30) REVERT: A 739 GLN cc_start: 0.9715 (mm-40) cc_final: 0.9284 (mm-40) REVERT: A 812 TYR cc_start: 0.9147 (t80) cc_final: 0.8919 (t80) REVERT: A 939 MET cc_start: 0.8152 (tmm) cc_final: 0.7913 (tmm) REVERT: A 943 TYR cc_start: 0.8815 (m-80) cc_final: 0.8242 (m-80) REVERT: A 981 TYR cc_start: 0.8859 (m-10) cc_final: 0.8617 (m-80) REVERT: A 1097 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8854 (tmtt) REVERT: A 1201 TYR cc_start: 0.9367 (m-80) cc_final: 0.9057 (m-80) REVERT: A 1204 PHE cc_start: 0.9278 (m-10) cc_final: 0.8867 (m-10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1017 time to fit residues: 14.6213 Evaluate side-chains 71 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 0.6980 chunk 111 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.066131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.055052 restraints weight = 179457.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056757 restraints weight = 90951.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057886 restraints weight = 57860.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.058621 restraints weight = 42421.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.059118 restraints weight = 33964.780| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13339 Z= 0.156 Angle : 0.550 8.114 18656 Z= 0.322 Chirality : 0.039 0.248 2141 Planarity : 0.005 0.079 1834 Dihedral : 18.661 80.859 3349 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 0.19 % Allowed : 0.76 % Favored : 99.05 % 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: -0.04 (0.24), residues: 1168 helix: 0.71 (0.21), residues: 612 sheet: -0.67 (0.57), residues: 76 loop : -0.79 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1171 TYR 0.013 0.001 TYR A 155 PHE 0.014 0.001 PHE A 970 TRP 0.020 0.001 TRP A1126 HIS 0.014 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (13339) covalent geometry : angle 0.55044 / 0.32 (18656) hydrogen bonds : bond 0.05256 / 3.35 ( 585) hydrogen bonds : angle 4.41070 / 3.03 ( 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 94 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.433 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 86 PHE cc_start: 0.9551 (m-80) cc_final: 0.9273 (m-10) REVERT: A 161 MET cc_start: 0.9411 (ttt) cc_final: 0.9090 (mtp) REVERT: A 321 MET cc_start: 0.9307 (mmp) cc_final: 0.9057 (mmp) REVERT: A 495 MET cc_start: 0.9535 (mpp) cc_final: 0.9133 (mpp) REVERT: A 534 MET cc_start: 0.5351 (ptm) cc_final: 0.4970 (ppp) REVERT: A 629 ARG cc_start: 0.9561 (ppt170) cc_final: 0.9349 (ptm-80) REVERT: A 631 MET cc_start: 0.9359 (mmp) cc_final: 0.9064 (mmm) REVERT: A 707 ASP cc_start: 0.9638 (m-30) cc_final: 0.9393 (m-30) REVERT: A 739 GLN cc_start: 0.9713 (mm-40) cc_final: 0.9292 (mm-40) REVERT: A 939 MET cc_start: 0.8170 (tmm) cc_final: 0.7855 (tmm) REVERT: A 943 TYR cc_start: 0.8848 (m-80) cc_final: 0.8273 (m-80) REVERT: A 981 TYR cc_start: 0.8877 (m-10) cc_final: 0.8636 (m-80) REVERT: A 1201 TYR cc_start: 0.9412 (m-80) cc_final: 0.9058 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1038 time to fit residues: 14.6408 Evaluate side-chains 66 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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: 1.9990 chunk 79 optimal weight: 0.2980 chunk 123 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 129 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 0.0270 chunk 117 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 overall best weight: 3.0644 ------------------------------------------------------------------------------- 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** ** 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 = 0.3588 r_free = 0.3588 target = 0.066461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.054861 restraints weight = 212450.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.056765 restraints weight = 101286.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.058004 restraints weight = 62298.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.058812 restraints weight = 44597.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.059358 restraints weight = 35075.374| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13339 Z= 0.133 Angle : 0.531 7.975 18656 Z= 0.309 Chirality : 0.038 0.251 2141 Planarity : 0.004 0.068 1834 Dihedral : 18.650 81.759 3349 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.74 % 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: 0.07 (0.24), residues: 1168 helix: 0.81 (0.21), residues: 612 sheet: -0.63 (0.55), residues: 81 loop : -0.76 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1171 TYR 0.017 0.001 TYR A 815 PHE 0.012 0.001 PHE A 626 TRP 0.017 0.001 TRP A1126 HIS 0.008 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (13339) covalent geometry : angle 0.53090 / 0.31 (18656) hydrogen bonds : bond 0.05021 / 3.18 ( 585) hydrogen bonds : angle 4.36088 / 3.01 ( 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 96 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.397 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 86 PHE cc_start: 0.9558 (m-80) cc_final: 0.9279 (m-10) REVERT: A 161 MET cc_start: 0.9378 (ttt) cc_final: 0.9082 (mtp) REVERT: A 321 MET cc_start: 0.9284 (mmp) cc_final: 0.9024 (mmp) REVERT: A 495 MET cc_start: 0.9524 (mpp) cc_final: 0.9125 (mpp) REVERT: A 534 MET cc_start: 0.5378 (ptm) cc_final: 0.5017 (ppp) REVERT: A 587 PHE cc_start: 0.8273 (m-80) cc_final: 0.7708 (m-80) REVERT: A 629 ARG cc_start: 0.9578 (ppt170) cc_final: 0.9320 (ptm-80) REVERT: A 631 MET cc_start: 0.9349 (mmp) cc_final: 0.9060 (mmm) REVERT: A 707 ASP cc_start: 0.9665 (m-30) cc_final: 0.9420 (m-30) REVERT: A 739 GLN cc_start: 0.9712 (mm-40) cc_final: 0.9287 (mm-40) REVERT: A 936 ASP cc_start: 0.9367 (m-30) cc_final: 0.9093 (m-30) REVERT: A 943 TYR cc_start: 0.8854 (m-80) cc_final: 0.8273 (m-80) REVERT: A 981 TYR cc_start: 0.8872 (m-10) cc_final: 0.8633 (m-80) REVERT: A 1169 MET cc_start: 0.7130 (tpt) cc_final: 0.6905 (tpt) REVERT: A 1201 TYR cc_start: 0.9412 (m-80) cc_final: 0.9034 (m-80) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1054 time to fit residues: 15.0273 Evaluate side-chains 73 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 2 optimal weight: 0.2980 chunk 128 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 overall best weight: 7.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 869 ASN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.050607 restraints weight = 248676.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052602 restraints weight = 113114.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.053864 restraints weight = 68911.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.054647 restraints weight = 49021.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.055179 restraints weight = 38693.462| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13339 Z= 0.213 Angle : 0.625 7.958 18656 Z= 0.358 Chirality : 0.040 0.239 2141 Planarity : 0.005 0.056 1834 Dihedral : 18.800 80.832 3349 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.14 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: -0.16 (0.24), residues: 1168 helix: 0.57 (0.21), residues: 607 sheet: 0.56 (0.75), residues: 49 loop : -0.94 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.023 0.002 TYR A 812 PHE 0.017 0.002 PHE A 970 TRP 0.016 0.002 TRP A1126 HIS 0.007 0.002 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 (13339) covalent geometry : angle 0.62457 / 0.36 (18656) hydrogen bonds : bond 0.06098 / 4.00 ( 585) hydrogen bonds : angle 4.61740 / 3.16 ( 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 89 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.339 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 60 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8244 (mm-30) REVERT: A 86 PHE cc_start: 0.9635 (m-80) cc_final: 0.9307 (m-10) REVERT: A 161 MET cc_start: 0.9403 (ttt) cc_final: 0.9157 (mtp) REVERT: A 321 MET cc_start: 0.9286 (mmp) cc_final: 0.8961 (mmp) REVERT: A 495 MET cc_start: 0.9509 (mpp) cc_final: 0.9133 (mpp) REVERT: A 534 MET cc_start: 0.5682 (ptm) cc_final: 0.5332 (ppp) REVERT: A 587 PHE cc_start: 0.8132 (m-80) cc_final: 0.7610 (m-80) REVERT: A 629 ARG cc_start: 0.9594 (ppt170) cc_final: 0.9319 (ptm-80) REVERT: A 631 MET cc_start: 0.9332 (mmp) cc_final: 0.9044 (mmm) REVERT: A 707 ASP cc_start: 0.9716 (m-30) cc_final: 0.9497 (m-30) REVERT: A 739 GLN cc_start: 0.9724 (mm-40) cc_final: 0.9327 (mm-40) REVERT: A 812 TYR cc_start: 0.9317 (t80) cc_final: 0.9097 (t80) REVERT: A 936 ASP cc_start: 0.9428 (m-30) cc_final: 0.9141 (m-30) REVERT: A 943 TYR cc_start: 0.8810 (m-80) cc_final: 0.8232 (m-80) REVERT: A 981 TYR cc_start: 0.8970 (m-10) cc_final: 0.8716 (m-80) REVERT: A 1089 MET cc_start: 0.8744 (mpp) cc_final: 0.8415 (mpp) REVERT: A 1169 MET cc_start: 0.7215 (tpt) cc_final: 0.6855 (tpt) REVERT: A 1201 TYR cc_start: 0.9439 (m-80) cc_final: 0.8985 (m-80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1124 time to fit residues: 14.8099 Evaluate side-chains 68 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 30.0000 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 119 optimal weight: 30.0000 chunk 124 optimal weight: 40.0000 chunk 123 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.061278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049716 restraints weight = 252328.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.051712 restraints weight = 114187.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.052957 restraints weight = 69610.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.053749 restraints weight = 49371.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054275 restraints weight = 38823.220| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13339 Z= 0.208 Angle : 0.624 10.815 18656 Z= 0.356 Chirality : 0.041 0.429 2141 Planarity : 0.005 0.049 1834 Dihedral : 18.911 81.808 3349 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % 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: -0.32 (0.24), residues: 1168 helix: 0.43 (0.21), residues: 607 sheet: 0.50 (0.75), residues: 49 loop : -1.01 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 71 TYR 0.017 0.002 TYR A1294 PHE 0.014 0.002 PHE A 626 TRP 0.015 0.002 TRP A1126 HIS 0.007 0.002 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 (13339) covalent geometry : angle 0.62395 / 0.36 (18656) hydrogen bonds : bond 0.05694 / 3.69 ( 585) hydrogen bonds : angle 4.64987 / 3.19 ( 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 84 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.456 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 86 PHE cc_start: 0.9628 (m-80) cc_final: 0.9352 (m-10) REVERT: A 161 MET cc_start: 0.9450 (ttt) cc_final: 0.9150 (mtp) REVERT: A 321 MET cc_start: 0.9275 (mmp) cc_final: 0.8944 (mmp) REVERT: A 495 MET cc_start: 0.9463 (mpp) cc_final: 0.9059 (mpp) REVERT: A 534 MET cc_start: 0.5325 (ptm) cc_final: 0.5045 (ppp) REVERT: A 564 LEU cc_start: 0.9365 (mm) cc_final: 0.8878 (mm) REVERT: A 587 PHE cc_start: 0.8069 (m-80) cc_final: 0.7567 (m-80) REVERT: A 629 ARG cc_start: 0.9601 (ppt170) cc_final: 0.9325 (ptm-80) REVERT: A 631 MET cc_start: 0.9296 (mmp) cc_final: 0.9007 (mmm) REVERT: A 707 ASP cc_start: 0.9730 (m-30) cc_final: 0.9521 (m-30) REVERT: A 739 GLN cc_start: 0.9719 (mm-40) cc_final: 0.9355 (mm-40) REVERT: A 812 TYR cc_start: 0.9222 (t80) cc_final: 0.9019 (t80) REVERT: A 936 ASP cc_start: 0.9444 (m-30) cc_final: 0.9173 (m-30) REVERT: A 943 TYR cc_start: 0.8820 (m-80) cc_final: 0.8255 (m-80) REVERT: A 981 TYR cc_start: 0.8974 (m-10) cc_final: 0.8726 (m-80) REVERT: A 1089 MET cc_start: 0.8820 (mpp) cc_final: 0.8454 (mpp) REVERT: A 1169 MET cc_start: 0.7612 (tpt) cc_final: 0.7170 (tpt) REVERT: A 1201 TYR cc_start: 0.9460 (m-80) cc_final: 0.8990 (m-80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1019 time to fit residues: 13.3509 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 : 0.260 ------------------------------------------------------------------------------- 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: 4.9990 chunk 87 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.051684 restraints weight = 226689.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.053669 restraints weight = 105456.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.054911 restraints weight = 64537.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.055687 restraints weight = 45884.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.056213 restraints weight = 36179.668| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4595 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= 0.138 Angle : 0.558 9.421 18656 Z= 0.322 Chirality : 0.040 0.365 2141 Planarity : 0.004 0.043 1834 Dihedral : 18.828 83.172 3349 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % 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: -0.10 (0.24), residues: 1168 helix: 0.66 (0.21), residues: 606 sheet: -0.70 (0.57), residues: 81 loop : -0.80 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.031 0.002 TYR A 517 PHE 0.014 0.001 PHE A1080 TRP 0.014 0.001 TRP A1126 HIS 0.008 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (13339) covalent geometry : angle 0.55770 / 0.32 (18656) hydrogen bonds : bond 0.05031 / 3.19 ( 585) hydrogen bonds : angle 4.43496 / 3.05 ( 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 86 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.365 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 86 PHE cc_start: 0.9655 (m-80) cc_final: 0.9351 (m-10) REVERT: A 161 MET cc_start: 0.9429 (ttt) cc_final: 0.9109 (mtp) REVERT: A 321 MET cc_start: 0.9245 (mmp) cc_final: 0.8944 (mmp) REVERT: A 495 MET cc_start: 0.9469 (mpp) cc_final: 0.9038 (mpp) REVERT: A 534 MET cc_start: 0.5353 (ptm) cc_final: 0.5079 (ppp) REVERT: A 564 LEU cc_start: 0.9261 (mm) cc_final: 0.8963 (mm) REVERT: A 629 ARG cc_start: 0.9580 (ppt170) cc_final: 0.9308 (ptm-80) REVERT: A 631 MET cc_start: 0.9268 (mmp) cc_final: 0.8975 (mmm) REVERT: A 707 ASP cc_start: 0.9717 (m-30) cc_final: 0.9497 (m-30) REVERT: A 739 GLN cc_start: 0.9718 (mm-40) cc_final: 0.9333 (mm-40) REVERT: A 936 ASP cc_start: 0.9431 (m-30) cc_final: 0.9157 (m-30) REVERT: A 943 TYR cc_start: 0.8810 (m-80) cc_final: 0.8543 (m-80) REVERT: A 981 TYR cc_start: 0.8933 (m-10) cc_final: 0.8673 (m-80) REVERT: A 1089 MET cc_start: 0.8738 (mpp) cc_final: 0.8484 (mpp) REVERT: A 1169 MET cc_start: 0.7451 (tpt) cc_final: 0.6955 (tpt) REVERT: A 1201 TYR cc_start: 0.9465 (m-80) cc_final: 0.8972 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1006 time to fit residues: 13.1920 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 : 0.430 ------------------------------------------------------------------------------- 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: 30.0000 chunk 77 optimal weight: 0.0870 chunk 129 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.0010 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 overall best weight: 3.0170 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.048805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035157 restraints weight = 193093.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.036747 restraints weight = 106268.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.037771 restraints weight = 72503.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038527 restraints weight = 56176.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.038978 restraints weight = 46726.208| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13339 Z= 0.137 Angle : 0.539 7.629 18656 Z= 0.313 Chirality : 0.039 0.385 2141 Planarity : 0.004 0.042 1834 Dihedral : 18.767 82.745 3349 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % 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: -0.01 (0.24), residues: 1168 helix: 0.71 (0.21), residues: 605 sheet: -0.65 (0.57), residues: 81 loop : -0.71 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.025 0.002 TYR A 517 PHE 0.014 0.001 PHE A1204 TRP 0.013 0.001 TRP A1126 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (13339) covalent geometry : angle 0.53944 / 0.31 (18656) hydrogen bonds : bond 0.04978 / 3.15 ( 585) hydrogen bonds : angle 4.34597 / 2.99 ( 1568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.52 seconds wall clock time: 38 minutes 6.50 seconds (2286.50 seconds total)