Starting phenix.real_space_refine on Sat Jul 4 06:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjj_45633/07_2026/9cjj_45633.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9408 atoms to isotropic. 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 57 5.49 5 S 27 5.16 5 C 7001 2.51 5 N 1922 2.21 5 O 2233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 11240 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 528 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 19} Chain: "A" Number of atoms: 10051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10051 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Conformer: "B" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} bond proxies already assigned to first conformer: 298 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DG D 19 " occ=0.90 ... (42 atoms not shown) pdb=" C4 B DG D 19 " occ=0.10 residue: pdb=" P A DA D 20 " occ=0.90 ... (40 atoms not shown) pdb=" C4 B DA D 20 " occ=0.10 Time building chain proxies: 2.66, per 1000 atoms: 0.24 Number of scatterers: 11240 At special positions: 0 Unit cell: (98.12, 110.385, 138.26, 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 27 16.00 P 57 15.00 O 2233 8.00 N 1922 7.00 C 7001 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 433.8 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 56.1% alpha, 10.3% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 50 through 68 removed outlier: 4.277A pdb=" N TYR A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.823A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.750A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 133 No H-bonds generated for 'chain 'A' and resid 132 through 133' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.523A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.529A pdb=" N ASP A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.787A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.235A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 325 through 344 removed outlier: 4.068A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.548A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.729A pdb=" N HIS A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 367 through 379 removed outlier: 4.678A pdb=" N GLU A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 395 removed outlier: 4.626A pdb=" N ARG A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 415 removed outlier: 3.566A pdb=" N LYS A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 451 removed outlier: 4.167A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.657A pdb=" N ILE A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 482 " --> pdb=" O TYR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 523 Proline residue: A 509 - end of helix removed outlier: 3.956A pdb=" N ASN A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.828A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.564A pdb=" N GLN A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.627A pdb=" N TYR A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Proline residue: A 716 - end of helix removed outlier: 3.789A pdb=" N TYR A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.616A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 819 through 831 removed outlier: 3.567A pdb=" N GLN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 removed outlier: 3.570A pdb=" N ARG A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 955 Processing helix chain 'A' and resid 957 through 987 removed outlier: 3.970A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.944A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.527A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1207 removed outlier: 3.569A pdb=" N ASP A1207 " --> pdb=" O LEU A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1284 removed outlier: 3.744A pdb=" N GLY A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1306 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.970A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 811 removed outlier: 5.233A pdb=" N ILE A 850 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 926 through 931 removed outlier: 3.703A pdb=" N GLU A 928 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 3.876A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1161 516 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.32 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: 3043 1.33 - 1.46: 2456 1.46 - 1.58: 5955 1.58 - 1.70: 111 1.70 - 1.82: 44 Bond restraints: 11609 Sorted by residual: bond pdb=" O5' 2YR C 7 " pdb=" P 2YR C 7 " ideal model delta sigma weight residual 1.721 1.600 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" C3' DG C 6 " pdb=" C2' DG C 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT C 12 " pdb=" C2' DT C 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" N ILE A 57 " pdb=" CA ILE A 57 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" C3' DC D 21 " pdb=" C2' DC D 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 ... (remaining 11604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15630 1.80 - 3.60: 273 3.60 - 5.40: 34 5.40 - 7.19: 4 7.19 - 8.99: 4 Bond angle restraints: 15945 Sorted by residual: angle pdb=" N TYR A 58 " pdb=" CA TYR A 58 " pdb=" C TYR A 58 " ideal model delta sigma weight residual 113.50 105.11 8.39 1.23e+00 6.61e-01 4.66e+01 angle pdb=" C LYS A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 120.54 112.09 8.45 1.35e+00 5.49e-01 3.91e+01 angle pdb=" O4' DA C 3 " pdb=" C4' DA C 3 " pdb=" C3' DA C 3 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.17e+01 angle pdb=" N LEU A 505 " pdb=" CA LEU A 505 " pdb=" C LEU A 505 " ideal model delta sigma weight residual 112.34 106.74 5.60 1.30e+00 5.92e-01 1.86e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 15940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 6598 35.61 - 71.21: 313 71.21 - 106.82: 16 106.82 - 142.42: 3 142.42 - 178.03: 2 Dihedral angle restraints: 6932 sinusoidal: 3270 harmonic: 3662 Sorted by residual: dihedral pdb=" O4' U B 16 " pdb=" C1' U B 16 " pdb=" N1 U B 16 " pdb=" C2 U B 16 " ideal model delta sinusoidal sigma weight residual 232.00 58.88 173.12 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" C4'A DG D 19 " pdb=" C3'A DG D 19 " pdb=" O3'A DG D 19 " pdb=" P A DA D 20 " ideal model delta sinusoidal sigma weight residual -140.00 38.03 -178.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ASP A 383 " pdb=" C ASP A 383 " pdb=" N THR A 384 " pdb=" CA THR A 384 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1389 0.045 - 0.090: 302 0.090 - 0.134: 75 0.134 - 0.179: 5 0.179 - 0.224: 4 Chirality restraints: 1775 Sorted by residual: chirality pdb=" CA TYR A 58 " pdb=" N TYR A 58 " pdb=" C TYR A 58 " pdb=" CB TYR A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' 2YR C 7 " pdb=" C2' 2YR C 7 " pdb=" N1 2YR C 7 " pdb=" O4' 2YR C 7 " both_signs ideal model delta sigma weight residual False 2.24 2.45 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1772 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2YR C 7 " 0.088 2.00e-02 2.50e+03 1.38e-01 4.74e+02 pdb=" C2 2YR C 7 " 0.018 2.00e-02 2.50e+03 pdb=" C4 2YR C 7 " -0.118 2.00e-02 2.50e+03 pdb=" C5 2YR C 7 " -0.124 2.00e-02 2.50e+03 pdb=" C6 2YR C 7 " -0.059 2.00e-02 2.50e+03 pdb=" C9 2YR C 7 " 0.326 2.00e-02 2.50e+03 pdb=" N1 2YR C 7 " 0.013 2.00e-02 2.50e+03 pdb=" N3 2YR C 7 " -0.049 2.00e-02 2.50e+03 pdb=" N4 2YR C 7 " -0.180 2.00e-02 2.50e+03 pdb=" O2 2YR C 7 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 502 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY A 502 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY A 502 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 503 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 916 " 0.007 2.00e-02 2.50e+03 1.23e-02 3.04e+00 pdb=" CG TYR A 916 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 916 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 916 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 916 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 916 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 916 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 916 " -0.006 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 0.45 - 1.34: 4 1.34 - 2.23: 26 2.23 - 3.12: 8423 3.12 - 4.01: 30078 4.01 - 4.90: 54642 Warning: very small nonbonded interaction distances. Nonbonded interactions: 93173 Sorted by model distance: nonbonded pdb=" CG ARG A 43 " pdb=" O SER A 161 " model vdw 0.454 3.440 nonbonded pdb=" CB TYR A 47 " pdb=" CE2 PHE A 162 " model vdw 0.754 3.740 nonbonded pdb=" CB TYR A 47 " pdb=" CZ PHE A 162 " model vdw 1.072 3.740 nonbonded pdb=" CE2 PHE A 165 " pdb=" CG LYS A 532 " model vdw 1.331 3.740 nonbonded pdb=" CD ARG A 43 " pdb=" O SER A 161 " model vdw 1.355 3.440 ... (remaining 93168 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=0.10 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 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 0.121 11611 Z= 0.234 Angle : 0.567 8.993 15945 Z= 0.372 Chirality : 0.041 0.224 1775 Planarity : 0.005 0.138 1842 Dihedral : 18.201 178.027 4562 Min Nonbonded Distance : 0.454 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.11 % Allowed : 1.84 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1232 helix: -0.39 (0.20), residues: 583 sheet: -0.49 (0.44), residues: 147 loop : -0.11 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1003 TYR 0.027 0.001 TYR A 916 PHE 0.019 0.001 PHE A1154 TRP 0.013 0.001 TRP A1085 HIS 0.002 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.23 (11609) covalent geometry : angle 0.56733 / 0.37 (15945) hydrogen bonds : bond 0.23263 / 21.76 ( 548) hydrogen bonds : angle 7.75211 / 7.91 ( 1522) Misc. bond : bond 0.03681 / 1.84 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8225 (tp) cc_final: 0.7962 (tp) REVERT: A 536 GLN cc_start: 0.7593 (mt0) cc_final: 0.7258 (mt0) REVERT: A 550 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7413 (mtpp) REVERT: A 593 MET cc_start: 0.8428 (ttm) cc_final: 0.8195 (ttm) REVERT: A 669 TYR cc_start: 0.6367 (t80) cc_final: 0.5972 (t80) REVERT: A 816 THR cc_start: 0.7800 (p) cc_final: 0.7599 (p) REVERT: A 893 ASN cc_start: 0.7664 (m-40) cc_final: 0.7341 (m-40) REVERT: A 1021 ASP cc_start: 0.7181 (m-30) cc_final: 0.6911 (m-30) REVERT: A 1087 THR cc_start: 0.7592 (p) cc_final: 0.7189 (m) outliers start: 12 outliers final: 1 residues processed: 193 average time/residue: 0.1295 time to fit residues: 34.1214 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.0040 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 534 ASN A1122 ASN A1303 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147742 restraints weight = 18867.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149729 restraints weight = 8773.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152531 restraints weight = 5917.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152454 restraints weight = 4883.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152471 restraints weight = 4197.079| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 11611 Z= 0.155 Angle : 0.607 8.598 15945 Z= 0.335 Chirality : 0.042 0.233 1775 Planarity : 0.005 0.037 1842 Dihedral : 18.778 174.804 2087 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.01 % Allowed : 8.57 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1232 helix: 0.74 (0.21), residues: 595 sheet: -0.36 (0.44), residues: 148 loop : -0.07 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 43 TYR 0.048 0.002 TYR A 47 PHE 0.066 0.002 PHE A 162 TRP 0.008 0.001 TRP A1085 HIS 0.006 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (11609) covalent geometry : angle 0.60697 / 0.34 (15945) hydrogen bonds : bond 0.06255 / 5.87 ( 548) hydrogen bonds : angle 5.26999 / 5.27 ( 1522) Misc. bond : bond 0.00268 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.6853 (m-30) cc_final: 0.6483 (m-30) REVERT: A 50 LEU cc_start: 0.7802 (tp) cc_final: 0.7501 (tp) REVERT: A 593 MET cc_start: 0.8395 (ttm) cc_final: 0.8189 (ttm) REVERT: A 786 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6691 (mt-10) REVERT: A 981 ASP cc_start: 0.6874 (t0) cc_final: 0.6648 (t0) REVERT: A 1021 ASP cc_start: 0.7032 (m-30) cc_final: 0.6727 (m-30) REVERT: A 1252 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7344 (mtm180) outliers start: 11 outliers final: 6 residues processed: 167 average time/residue: 0.1306 time to fit residues: 29.7460 Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 48 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 HIS A1122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145767 restraints weight = 21075.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146242 restraints weight = 10345.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147579 restraints weight = 8220.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148224 restraints weight = 6204.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.148192 restraints weight = 5750.977| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11611 Z= 0.155 Angle : 0.554 6.630 15945 Z= 0.305 Chirality : 0.042 0.186 1775 Planarity : 0.004 0.068 1842 Dihedral : 18.734 175.125 2085 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.20 % Allowed : 11.34 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.74 (0.25), residues: 1232 helix: 1.24 (0.21), residues: 600 sheet: -0.40 (0.44), residues: 148 loop : -0.03 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1003 TYR 0.043 0.002 TYR A 47 PHE 0.045 0.002 PHE A 162 TRP 0.009 0.001 TRP A1085 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (11609) covalent geometry : angle 0.55394 / 0.31 (15945) hydrogen bonds : bond 0.05041 / 4.60 ( 548) hydrogen bonds : angle 4.75993 / 4.76 ( 1522) Misc. bond : bond 0.00279 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.6770 (m-30) cc_final: 0.6373 (m-30) REVERT: A 50 LEU cc_start: 0.7819 (tp) cc_final: 0.7534 (tp) REVERT: A 339 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6565 (tp) REVERT: A 439 THR cc_start: 0.6644 (p) cc_final: 0.6413 (p) REVERT: A 786 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6577 (mt-10) REVERT: A 893 ASN cc_start: 0.7764 (m-40) cc_final: 0.7512 (m-40) REVERT: A 993 GLU cc_start: 0.7333 (pm20) cc_final: 0.7059 (pt0) REVERT: A 1021 ASP cc_start: 0.6992 (m-30) cc_final: 0.6713 (m-30) REVERT: A 1220 ARG cc_start: 0.5833 (mmm-85) cc_final: 0.5610 (tpp80) REVERT: A 1250 ASP cc_start: 0.6455 (t0) cc_final: 0.6219 (t0) outliers start: 13 outliers final: 6 residues processed: 169 average time/residue: 0.1313 time to fit residues: 30.0377 Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 35 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 HIS A1122 ASN A1296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.184586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146830 restraints weight = 26716.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146031 restraints weight = 14270.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148309 restraints weight = 9196.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148051 restraints weight = 6767.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148276 restraints weight = 6238.613| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11611 Z= 0.178 Angle : 0.550 6.590 15945 Z= 0.302 Chirality : 0.042 0.211 1775 Planarity : 0.004 0.064 1842 Dihedral : 18.593 174.305 2085 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.66 % Allowed : 12.72 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.87 (0.25), residues: 1232 helix: 1.45 (0.22), residues: 601 sheet: -0.58 (0.42), residues: 156 loop : -0.01 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1003 TYR 0.029 0.002 TYR A 47 PHE 0.033 0.002 PHE A 162 TRP 0.010 0.001 TRP A1085 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (11609) covalent geometry : angle 0.54979 / 0.30 (15945) hydrogen bonds : bond 0.04435 / 4.04 ( 548) hydrogen bonds : angle 4.51419 / 4.49 ( 1522) Misc. bond : bond 0.00145 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.6767 (m-30) cc_final: 0.6393 (m-30) REVERT: A 50 LEU cc_start: 0.7968 (tp) cc_final: 0.7747 (tp) REVERT: A 339 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6958 (tp) REVERT: A 526 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: A 528 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7879 (t) REVERT: A 786 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 806 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: A 993 GLU cc_start: 0.7362 (pm20) cc_final: 0.7147 (pt0) REVERT: A 1002 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7640 (ttmm) REVERT: A 1021 ASP cc_start: 0.7012 (m-30) cc_final: 0.6720 (m-30) REVERT: A 1115 LEU cc_start: 0.8172 (tp) cc_final: 0.7940 (tp) REVERT: A 1118 LYS cc_start: 0.7067 (mmtm) cc_final: 0.6701 (mttm) REVERT: A 1250 ASP cc_start: 0.6409 (t0) cc_final: 0.6101 (t0) outliers start: 18 outliers final: 10 residues processed: 175 average time/residue: 0.1234 time to fit residues: 29.5799 Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 102 optimal weight: 0.0270 chunk 123 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146103 restraints weight = 17322.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146417 restraints weight = 9185.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148263 restraints weight = 7075.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149248 restraints weight = 5417.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149052 restraints weight = 4664.087| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3748 r_free = 0.3748 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11611 Z= 0.141 Angle : 0.518 6.711 15945 Z= 0.285 Chirality : 0.041 0.223 1775 Planarity : 0.004 0.051 1842 Dihedral : 18.564 174.492 2085 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.03 % Allowed : 13.09 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.25), residues: 1232 helix: 1.63 (0.22), residues: 601 sheet: -0.59 (0.42), residues: 156 loop : 0.03 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1220 TYR 0.019 0.002 TYR A 595 PHE 0.034 0.002 PHE A1103 TRP 0.005 0.001 TRP A1085 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11609) covalent geometry : angle 0.51799 / 0.29 (15945) hydrogen bonds : bond 0.04031 / 3.65 ( 548) hydrogen bonds : angle 4.36988 / 4.35 ( 1522) Misc. bond : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7704 (m-30) cc_final: 0.7359 (m-30) REVERT: A 45 ASP cc_start: 0.6773 (m-30) cc_final: 0.6390 (m-30) REVERT: A 50 LEU cc_start: 0.7891 (tp) cc_final: 0.7645 (tp) REVERT: A 235 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6710 (m) REVERT: A 339 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6930 (tp) REVERT: A 439 THR cc_start: 0.7053 (p) cc_final: 0.6811 (p) REVERT: A 526 TYR cc_start: 0.6056 (OUTLIER) cc_final: 0.5559 (m-80) REVERT: A 528 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7931 (t) REVERT: A 736 GLU cc_start: 0.7274 (tp30) cc_final: 0.6954 (tp30) REVERT: A 786 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6568 (mt-10) REVERT: A 806 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7096 (mtt) REVERT: A 993 GLU cc_start: 0.7320 (pm20) cc_final: 0.7118 (pt0) REVERT: A 1002 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7623 (ttmt) REVERT: A 1021 ASP cc_start: 0.6983 (m-30) cc_final: 0.6701 (m-30) REVERT: A 1115 LEU cc_start: 0.8158 (tp) cc_final: 0.7950 (tp) REVERT: A 1118 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6693 (mttm) REVERT: A 1238 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.6708 (t0) REVERT: A 1250 ASP cc_start: 0.6449 (t0) cc_final: 0.6143 (t0) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.1222 time to fit residues: 29.7320 Evaluate side-chains 186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.185138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145882 restraints weight = 19482.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146170 restraints weight = 9795.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148148 restraints weight = 7463.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149111 restraints weight = 5390.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149134 restraints weight = 5016.112| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11611 Z= 0.136 Angle : 0.513 6.757 15945 Z= 0.281 Chirality : 0.041 0.227 1775 Planarity : 0.004 0.048 1842 Dihedral : 18.545 174.633 2085 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 14.29 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.11 (0.25), residues: 1232 helix: 1.75 (0.22), residues: 603 sheet: -0.65 (0.43), residues: 146 loop : 0.01 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1003 TYR 0.019 0.002 TYR A 595 PHE 0.033 0.001 PHE A1103 TRP 0.005 0.001 TRP A 676 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11609) covalent geometry : angle 0.51337 / 0.28 (15945) hydrogen bonds : bond 0.03872 / 3.52 ( 548) hydrogen bonds : angle 4.29749 / 4.27 ( 1522) Misc. bond : bond 0.00123 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8483 (p) REVERT: A 40 ASP cc_start: 0.7657 (m-30) cc_final: 0.7303 (m-30) REVERT: A 43 ARG cc_start: 0.6308 (ttm170) cc_final: 0.5964 (ttm170) REVERT: A 45 ASP cc_start: 0.6789 (m-30) cc_final: 0.6427 (m-30) REVERT: A 50 LEU cc_start: 0.7894 (tp) cc_final: 0.7642 (tp) REVERT: A 235 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6713 (m) REVERT: A 339 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6938 (tp) REVERT: A 439 THR cc_start: 0.7066 (p) cc_final: 0.6861 (p) REVERT: A 526 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: A 736 GLU cc_start: 0.7252 (tp30) cc_final: 0.6947 (tp30) REVERT: A 806 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7103 (mtt) REVERT: A 1002 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7613 (ttmt) REVERT: A 1021 ASP cc_start: 0.6971 (m-30) cc_final: 0.6685 (m-30) REVERT: A 1095 LYS cc_start: 0.7199 (mmmm) cc_final: 0.6980 (mmmt) REVERT: A 1115 LEU cc_start: 0.8160 (tp) cc_final: 0.7952 (tp) REVERT: A 1118 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6690 (mttm) outliers start: 17 outliers final: 9 residues processed: 178 average time/residue: 0.1293 time to fit residues: 31.3791 Evaluate side-chains 183 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 925 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 95 optimal weight: 0.7980 chunk 111 optimal weight: 0.0020 chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 76 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 0.0050 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146855 restraints weight = 24998.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147101 restraints weight = 11899.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149358 restraints weight = 8462.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149461 restraints weight = 6553.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149437 restraints weight = 6146.461| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11611 Z= 0.115 Angle : 0.498 7.012 15945 Z= 0.274 Chirality : 0.040 0.237 1775 Planarity : 0.004 0.035 1842 Dihedral : 18.491 175.183 2085 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.03 % Allowed : 13.36 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.28 (0.25), residues: 1232 helix: 1.92 (0.22), residues: 603 sheet: -0.55 (0.43), residues: 156 loop : 0.05 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1003 TYR 0.017 0.001 TYR A 595 PHE 0.031 0.001 PHE A1103 TRP 0.005 0.001 TRP A 676 HIS 0.004 0.000 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11609) covalent geometry : angle 0.49763 / 0.27 (15945) hydrogen bonds : bond 0.03584 / 3.25 ( 548) hydrogen bonds : angle 4.19205 / 4.15 ( 1522) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (p) REVERT: A 40 ASP cc_start: 0.7657 (m-30) cc_final: 0.7375 (m-30) REVERT: A 50 LEU cc_start: 0.7830 (tp) cc_final: 0.7571 (tp) REVERT: A 235 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6738 (m) REVERT: A 339 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6914 (tp) REVERT: A 526 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: A 567 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 736 GLU cc_start: 0.7241 (tp30) cc_final: 0.6957 (tp30) REVERT: A 806 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7058 (mtt) REVERT: A 912 ARG cc_start: 0.6878 (mmp80) cc_final: 0.6492 (mmp80) REVERT: A 1021 ASP cc_start: 0.6925 (m-30) cc_final: 0.6613 (m-30) REVERT: A 1095 LYS cc_start: 0.7216 (mmmm) cc_final: 0.6999 (mmmt) REVERT: A 1238 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.6726 (t0) REVERT: A 1250 ASP cc_start: 0.6391 (t0) cc_final: 0.6096 (t0) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.1187 time to fit residues: 29.2662 Evaluate side-chains 181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain A residue 1244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 120 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 64 optimal weight: 0.0010 chunk 20 optimal weight: 0.0170 chunk 93 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149450 restraints weight = 16536.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150779 restraints weight = 9450.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152289 restraints weight = 6234.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152272 restraints weight = 5247.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152459 restraints weight = 5024.918| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11611 Z= 0.104 Angle : 0.502 7.836 15945 Z= 0.274 Chirality : 0.039 0.241 1775 Planarity : 0.004 0.035 1842 Dihedral : 18.413 175.526 2085 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.03 % Allowed : 14.19 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.37 (0.25), residues: 1232 helix: 1.96 (0.22), residues: 606 sheet: -0.50 (0.43), residues: 156 loop : 0.11 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1003 TYR 0.016 0.001 TYR A1106 PHE 0.029 0.001 PHE A1103 TRP 0.005 0.001 TRP A 676 HIS 0.004 0.000 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11609) covalent geometry : angle 0.50240 / 0.27 (15945) hydrogen bonds : bond 0.03492 / 3.18 ( 548) hydrogen bonds : angle 4.13728 / 4.13 ( 1522) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 43 ARG cc_start: 0.6357 (ttm170) cc_final: 0.6006 (ttm170) REVERT: A 50 LEU cc_start: 0.7965 (tp) cc_final: 0.7691 (tp) REVERT: A 235 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6560 (m) REVERT: A 339 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6918 (tp) REVERT: A 526 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: A 567 ILE cc_start: 0.8238 (pt) cc_final: 0.7932 (mt) REVERT: A 736 GLU cc_start: 0.7130 (tp30) cc_final: 0.6886 (tp30) REVERT: A 806 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7104 (mtt) REVERT: A 1021 ASP cc_start: 0.6850 (m-30) cc_final: 0.6551 (m-30) outliers start: 22 outliers final: 12 residues processed: 176 average time/residue: 0.1186 time to fit residues: 29.1331 Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 GLN ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146388 restraints weight = 18557.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146870 restraints weight = 9271.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149900 restraints weight = 7106.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150244 restraints weight = 5137.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150144 restraints weight = 4300.230| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11611 Z= 0.141 Angle : 0.525 7.755 15945 Z= 0.284 Chirality : 0.041 0.245 1775 Planarity : 0.004 0.035 1842 Dihedral : 18.363 175.203 2085 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.84 % Allowed : 14.65 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.38 (0.25), residues: 1232 helix: 1.97 (0.21), residues: 608 sheet: -0.55 (0.42), residues: 156 loop : 0.14 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1003 TYR 0.020 0.002 TYR A 595 PHE 0.029 0.001 PHE A1103 TRP 0.003 0.001 TRP A 676 HIS 0.003 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11609) covalent geometry : angle 0.52511 / 0.28 (15945) hydrogen bonds : bond 0.03598 / 3.31 ( 548) hydrogen bonds : angle 4.12067 / 4.10 ( 1522) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 26 LYS cc_start: 0.7358 (ptmt) cc_final: 0.7053 (pttt) REVERT: A 50 LEU cc_start: 0.7711 (tp) cc_final: 0.7438 (tp) REVERT: A 235 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6700 (m) REVERT: A 526 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: A 567 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 603 LYS cc_start: 0.8017 (pttt) cc_final: 0.7808 (pttt) REVERT: A 736 GLU cc_start: 0.7386 (tp30) cc_final: 0.6845 (tp30) REVERT: A 806 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7081 (mtt) REVERT: A 1021 ASP cc_start: 0.7053 (m-30) cc_final: 0.6740 (m-30) REVERT: A 1095 LYS cc_start: 0.7305 (mmmt) cc_final: 0.7076 (mmmt) REVERT: A 1118 LYS cc_start: 0.7087 (mmtm) cc_final: 0.6695 (mttm) outliers start: 20 outliers final: 14 residues processed: 172 average time/residue: 0.1135 time to fit residues: 27.0054 Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.185372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144310 restraints weight = 16799.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147843 restraints weight = 8274.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150015 restraints weight = 5430.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.150898 restraints weight = 4285.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151761 restraints weight = 3845.196| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 11611 Z= 0.197 Angle : 0.814 59.199 15945 Z= 0.472 Chirality : 0.044 0.602 1775 Planarity : 0.004 0.035 1842 Dihedral : 18.361 175.179 2085 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.94 % Allowed : 15.12 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.38 (0.25), residues: 1232 helix: 1.97 (0.21), residues: 608 sheet: -0.55 (0.42), residues: 156 loop : 0.14 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1003 TYR 0.019 0.002 TYR A 595 PHE 0.030 0.002 PHE A1103 TRP 0.009 0.001 TRP A 483 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (11609) covalent geometry : angle 0.81378 / 0.47 (15945) hydrogen bonds : bond 0.03602 / 3.31 ( 548) hydrogen bonds : angle 4.11859 / 4.09 ( 1522) Misc. bond : bond 0.00158 / 0.08 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 26 LYS cc_start: 0.7307 (ptmt) cc_final: 0.6990 (pttt) REVERT: A 50 LEU cc_start: 0.7858 (tp) cc_final: 0.7563 (tp) REVERT: A 235 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6653 (m) REVERT: A 526 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: A 567 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7950 (mt) REVERT: A 736 GLU cc_start: 0.7280 (tp30) cc_final: 0.6741 (tp30) REVERT: A 806 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7102 (mtt) REVERT: A 1021 ASP cc_start: 0.6943 (m-30) cc_final: 0.6635 (m-30) REVERT: A 1095 LYS cc_start: 0.7196 (mmmt) cc_final: 0.6991 (mmmt) REVERT: A 1118 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6659 (mttm) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.1071 time to fit residues: 25.4293 Evaluate side-chains 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1192 VAL Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1244 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 16 optimal weight: 0.0070 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1238 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.185290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144366 restraints weight = 16554.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147880 restraints weight = 8220.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150054 restraints weight = 5402.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151029 restraints weight = 4270.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151926 restraints weight = 3820.043| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 11611 Z= 0.197 Angle : 0.814 59.199 15945 Z= 0.472 Chirality : 0.044 0.602 1775 Planarity : 0.004 0.035 1842 Dihedral : 18.361 175.179 2085 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.84 % Allowed : 15.39 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.38 (0.25), residues: 1232 helix: 1.97 (0.21), residues: 608 sheet: -0.55 (0.42), residues: 156 loop : 0.14 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1003 TYR 0.019 0.002 TYR A 595 PHE 0.030 0.002 PHE A1103 TRP 0.009 0.001 TRP A 483 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (11609) covalent geometry : angle 0.81378 / 0.47 (15945) hydrogen bonds : bond 0.03602 / 3.31 ( 548) hydrogen bonds : angle 4.11859 / 4.09 ( 1522) Misc. bond : bond 0.00158 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.53 seconds wall clock time: 38 minutes 10.90 seconds (2290.90 seconds total)