Starting phenix.real_space_refine on Sat Aug 23 14:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfn_40445/08_2025/8sfn_40445.map" } resolution = 3.3 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= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 103 5.49 5 S 26 5.16 5 C 7836 2.51 5 N 2195 2.21 5 O 2647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12807 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1302, 10652 Classifications: {'peptide': 1302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1252} Chain breaks: 1 Chain: "B" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 761 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 29} Chain: "C" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Time building chain proxies: 2.84, per 1000 atoms: 0.22 Number of scatterers: 12807 At special positions: 0 Unit cell: (102.484, 94.9848, 135.812, 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 26 16.00 P 103 15.00 O 2647 8.00 N 2195 7.00 C 7836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 494.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 54.3% alpha, 13.0% beta 37 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.544A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.657A pdb=" N SER A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.934A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.031A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.917A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 138 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 138' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 197 through 215 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.875A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.594A pdb=" N VAL A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.935A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 removed outlier: 4.001A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.906A pdb=" N ILE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 413 removed outlier: 4.036A pdb=" N VAL A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.523A pdb=" N ILE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.997A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 484 removed outlier: 3.811A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 507 through 522 removed outlier: 4.322A pdb=" N LEU A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.671A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 639 through 647 removed outlier: 4.798A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 removed outlier: 3.770A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.505A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.878A 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: 3.741A 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 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 4.221A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 4.391A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1010 through 1024 removed outlier: 3.628A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 removed outlier: 3.566A pdb=" N GLU A1181 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1206 removed outlier: 3.979A pdb=" N ASN A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 removed outlier: 3.882A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1283 Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 719 through 727 removed outlier: 5.658A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.737A pdb=" N ILE A 265 " --> pdb=" O ILE A 274 " (cutoff:3.500A) 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: 3.766A pdb=" N ASN A 808 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.081A 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 930 removed outlier: 6.729A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 918 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1106 removed outlier: 6.701A pdb=" N HIS A1116 " --> pdb=" O ASP A1102 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A1104 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A1114 " --> pdb=" O LEU A1104 " (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 1161 through 1162 removed outlier: 3.590A pdb=" N VAL A1161 " --> pdb=" O ARG A1174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1227 removed outlier: 4.290A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3357 1.34 - 1.46: 3240 1.46 - 1.58: 6456 1.58 - 1.70: 207 1.70 - 1.82: 44 Bond restraints: 13304 Sorted by residual: bond pdb=" CB PRO A1178 " pdb=" CG PRO A1178 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.07e+00 bond pdb=" CB GLU A 857 " pdb=" CG GLU A 857 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.02e+00 bond pdb=" CG1 ILE A 979 " pdb=" CD1 ILE A 979 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.91e+00 bond pdb=" CB PHE A1249 " pdb=" CG PHE A1249 " ideal model delta sigma weight residual 1.502 1.552 -0.050 2.30e-02 1.89e+03 4.64e+00 bond pdb=" CB PRO A1042 " pdb=" CG PRO A1042 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.49e+00 ... (remaining 13299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 18270 5.65 - 11.29: 142 11.29 - 16.94: 16 16.94 - 22.59: 5 22.59 - 28.23: 1 Bond angle restraints: 18434 Sorted by residual: angle pdb=" CA PRO A1178 " pdb=" N PRO A1178 " pdb=" CD PRO A1178 " ideal model delta sigma weight residual 112.00 96.92 15.08 1.40e+00 5.10e-01 1.16e+02 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 136.23 -28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O3' DA D 20 " pdb=" P DA D 21 " pdb=" OP1 DA D 21 " ideal model delta sigma weight residual 108.00 129.72 -21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" O3' DA D 21 " pdb=" P DG D 22 " pdb=" OP1 DG D 22 " ideal model delta sigma weight residual 108.00 126.71 -18.71 3.00e+00 1.11e-01 3.89e+01 angle pdb=" CA ARG A 386 " pdb=" CB ARG A 386 " pdb=" CG ARG A 386 " ideal model delta sigma weight residual 114.10 126.42 -12.32 2.00e+00 2.50e-01 3.79e+01 ... (remaining 18429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 7289 35.13 - 70.27: 570 70.27 - 105.40: 33 105.40 - 140.53: 2 140.53 - 175.66: 5 Dihedral angle restraints: 7899 sinusoidal: 4053 harmonic: 3846 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 47.25 152.75 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 67.59 132.41 1 1.50e+01 4.44e-03 7.14e+01 dihedral pdb=" CA TYR A 746 " pdb=" C TYR A 746 " pdb=" N ASN A 747 " pdb=" CA ASN A 747 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 7896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 2002 0.152 - 0.305: 25 0.305 - 0.457: 20 0.457 - 0.610: 3 0.610 - 0.762: 3 Chirality restraints: 2053 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.11 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" P DA D 21 " pdb=" OP1 DA D 21 " pdb=" OP2 DA D 21 " pdb=" O5' DA D 21 " both_signs ideal model delta sigma weight residual True 2.35 -3.02 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" P DG D 22 " pdb=" OP1 DG D 22 " pdb=" OP2 DG D 22 " pdb=" O5' DG D 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.35e+00 ... (remaining 2050 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1177 " -0.134 5.00e-02 4.00e+02 1.89e-01 5.69e+01 pdb=" N PRO A1178 " 0.325 5.00e-02 4.00e+02 pdb=" CA PRO A1178 " -0.101 5.00e-02 4.00e+02 pdb=" CD PRO A1178 " -0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1041 " 0.068 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO A1042 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A1042 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1042 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 184 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP A 184 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP A 184 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 185 " -0.021 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 811 2.73 - 3.27: 12732 3.27 - 3.82: 23450 3.82 - 4.36: 27512 4.36 - 4.90: 42953 Nonbonded interactions: 107458 Sorted by model distance: nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.188 3.040 nonbonded pdb=" O CYS A 334 " pdb=" OG1 THR A 338 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 595 " pdb=" O LEU A 781 " model vdw 2.277 3.040 nonbonded pdb=" O TYR A 11 " pdb=" NE2 GLN A1044 " model vdw 2.292 3.120 nonbonded pdb=" O ILE A1073 " pdb=" ND2 ASN A1265 " model vdw 2.299 3.120 ... (remaining 107453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.920 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.005 0.133 13304 Z= 0.228 Angle : 1.222 28.234 18434 Z= 0.573 Chirality : 0.072 0.762 2053 Planarity : 0.008 0.189 1998 Dihedral : 21.535 175.662 5409 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.26 % Allowed : 26.93 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.22), residues: 1298 helix: -0.61 (0.19), residues: 613 sheet: -0.69 (0.42), residues: 148 loop : -1.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 386 TYR 0.039 0.002 TYR A 971 PHE 0.029 0.002 PHE A 999 TRP 0.057 0.003 TRP A 483 HIS 0.024 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00536 (13304) covalent geometry : angle 1.22231 (18434) hydrogen bonds : bond 0.15103 ( 606) hydrogen bonds : angle 7.07488 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 999 PHE cc_start: 0.6747 (t80) cc_final: 0.5837 (t80) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.0986 time to fit residues: 15.2772 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 972 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 9 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 913 ASN A 929 GLN A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 ASN A1303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.070444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047874 restraints weight = 67872.611| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.11 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13304 Z= 0.237 Angle : 0.701 10.842 18434 Z= 0.372 Chirality : 0.042 0.172 2053 Planarity : 0.005 0.100 1998 Dihedral : 22.036 175.365 2718 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.09 % Allowed : 23.16 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.23), residues: 1298 helix: 0.70 (0.20), residues: 626 sheet: -0.88 (0.45), residues: 134 loop : -0.55 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 386 TYR 0.022 0.002 TYR A 61 PHE 0.020 0.002 PHE A 198 TRP 0.011 0.001 TRP A1258 HIS 0.012 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00505 (13304) covalent geometry : angle 0.70056 (18434) hydrogen bonds : bond 0.04399 ( 606) hydrogen bonds : angle 4.94929 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8216 (mm) REVERT: A 507 MET cc_start: 0.8948 (mmm) cc_final: 0.8646 (mmm) REVERT: A 624 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9046 (t) REVERT: A 1006 ILE cc_start: 0.8707 (mp) cc_final: 0.8504 (mp) outliers start: 36 outliers final: 15 residues processed: 105 average time/residue: 0.1055 time to fit residues: 16.8947 Evaluate side-chains 87 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 27 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.070990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048646 restraints weight = 68825.495| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 5.19 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13304 Z= 0.153 Angle : 0.617 10.400 18434 Z= 0.327 Chirality : 0.039 0.164 2053 Planarity : 0.004 0.069 1998 Dihedral : 21.949 179.927 2716 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.49 % Allowed : 22.98 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1298 helix: 1.13 (0.21), residues: 626 sheet: -0.86 (0.44), residues: 137 loop : -0.41 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 386 TYR 0.019 0.001 TYR A 595 PHE 0.020 0.001 PHE A 999 TRP 0.008 0.001 TRP A 765 HIS 0.009 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00334 (13304) covalent geometry : angle 0.61740 (18434) hydrogen bonds : bond 0.03638 ( 606) hydrogen bonds : angle 4.55114 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 61 TYR cc_start: 0.9009 (t80) cc_final: 0.8772 (t80) REVERT: A 319 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 507 MET cc_start: 0.9068 (mmm) cc_final: 0.8814 (mmm) REVERT: A 732 MET cc_start: 0.9151 (tmm) cc_final: 0.8792 (tmm) REVERT: A 1016 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8286 (mp0) outliers start: 29 outliers final: 13 residues processed: 105 average time/residue: 0.1074 time to fit residues: 16.8103 Evaluate side-chains 82 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044556 restraints weight = 70804.534| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.01 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 13304 Z= 0.348 Angle : 0.755 9.961 18434 Z= 0.406 Chirality : 0.045 0.180 2053 Planarity : 0.005 0.053 1998 Dihedral : 22.299 178.277 2716 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.12 % Allowed : 22.21 % Favored : 73.67 % 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 aren not related in a simple way. whole: 0.16 (0.23), residues: 1298 helix: 0.92 (0.20), residues: 629 sheet: -0.59 (0.45), residues: 135 loop : -0.60 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 210 TYR 0.025 0.003 TYR A 61 PHE 0.023 0.002 PHE A 198 TRP 0.010 0.002 TRP A1258 HIS 0.006 0.002 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00734 (13304) covalent geometry : angle 0.75511 (18434) hydrogen bonds : bond 0.05009 ( 606) hydrogen bonds : angle 4.94320 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 73 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.9748 (OUTLIER) cc_final: 0.9501 (mmmt) REVERT: A 165 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.9139 (t80) REVERT: A 174 GLU cc_start: 0.9612 (mm-30) cc_final: 0.9393 (mm-30) REVERT: A 319 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 507 MET cc_start: 0.9334 (mmm) cc_final: 0.9107 (mmm) REVERT: A 624 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9024 (t) REVERT: A 780 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8177 (tttm) REVERT: A 868 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8321 (mmtp) REVERT: A 1016 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 1055 MET cc_start: 0.8839 (tmm) cc_final: 0.8627 (tmm) REVERT: A 1083 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8737 (m-10) REVERT: A 1238 ASN cc_start: 0.9549 (OUTLIER) cc_final: 0.8283 (m-40) outliers start: 48 outliers final: 27 residues processed: 115 average time/residue: 0.1103 time to fit residues: 18.9640 Evaluate side-chains 104 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 868 LYS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 11 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.068299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045921 restraints weight = 70301.482| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 5.15 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13304 Z= 0.218 Angle : 0.657 11.131 18434 Z= 0.349 Chirality : 0.041 0.172 2053 Planarity : 0.004 0.049 1998 Dihedral : 22.154 177.539 2716 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.52 % Allowed : 23.33 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.24), residues: 1298 helix: 1.18 (0.21), residues: 626 sheet: -0.94 (0.42), residues: 149 loop : -0.46 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 210 TYR 0.019 0.002 TYR A 971 PHE 0.022 0.002 PHE A 999 TRP 0.013 0.001 TRP A1298 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00470 (13304) covalent geometry : angle 0.65688 (18434) hydrogen bonds : bond 0.03918 ( 606) hydrogen bonds : angle 4.62809 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 73 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8517 (tp30) cc_final: 0.8279 (tp30) REVERT: A 319 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 507 MET cc_start: 0.9279 (mmm) cc_final: 0.9066 (mmm) REVERT: A 732 MET cc_start: 0.9196 (tmm) cc_final: 0.8881 (tmm) REVERT: A 1016 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: A 1133 MET cc_start: 0.8422 (mmm) cc_final: 0.8213 (mmm) REVERT: A 1238 ASN cc_start: 0.9542 (OUTLIER) cc_final: 0.8204 (m-40) outliers start: 41 outliers final: 25 residues processed: 105 average time/residue: 0.0995 time to fit residues: 15.9026 Evaluate side-chains 95 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1238 ASN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 0.0170 chunk 23 optimal weight: 0.1980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.070577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.048708 restraints weight = 68948.609| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.17 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13304 Z= 0.126 Angle : 0.615 11.750 18434 Z= 0.319 Chirality : 0.039 0.194 2053 Planarity : 0.004 0.043 1998 Dihedral : 21.789 178.266 2716 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.92 % Allowed : 24.61 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.24), residues: 1298 helix: 1.41 (0.21), residues: 623 sheet: -0.92 (0.41), residues: 152 loop : -0.27 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 43 TYR 0.030 0.001 TYR A 971 PHE 0.016 0.001 PHE A 999 TRP 0.012 0.001 TRP A1298 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00276 (13304) covalent geometry : angle 0.61471 (18434) hydrogen bonds : bond 0.03341 ( 606) hydrogen bonds : angle 4.30829 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8519 (tp30) cc_final: 0.8200 (tp30) REVERT: A 319 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 507 MET cc_start: 0.9333 (mmm) cc_final: 0.9129 (mmm) REVERT: A 732 MET cc_start: 0.9190 (tmm) cc_final: 0.8834 (tmm) REVERT: A 1016 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: A 1176 LEU cc_start: 0.9113 (tt) cc_final: 0.8810 (mp) outliers start: 34 outliers final: 19 residues processed: 112 average time/residue: 0.1162 time to fit residues: 19.4186 Evaluate side-chains 98 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 0.0010 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.069865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047729 restraints weight = 69682.676| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.15 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13304 Z= 0.147 Angle : 0.627 12.193 18434 Z= 0.327 Chirality : 0.040 0.199 2053 Planarity : 0.004 0.049 1998 Dihedral : 21.800 179.621 2716 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.83 % Allowed : 24.61 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1298 helix: 1.43 (0.21), residues: 625 sheet: -0.78 (0.42), residues: 143 loop : -0.25 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1174 TYR 0.035 0.002 TYR A 971 PHE 0.013 0.001 PHE A 198 TRP 0.011 0.001 TRP A 765 HIS 0.006 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00328 (13304) covalent geometry : angle 0.62677 (18434) hydrogen bonds : bond 0.03456 ( 606) hydrogen bonds : angle 4.32921 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 78 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8544 (tp30) cc_final: 0.8181 (tp30) REVERT: A 319 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8352 (mm) REVERT: A 732 MET cc_start: 0.9192 (tmm) cc_final: 0.8843 (tmm) REVERT: A 1016 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8300 (mp0) outliers start: 33 outliers final: 26 residues processed: 105 average time/residue: 0.1100 time to fit residues: 17.4702 Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 11 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN A 946 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.068312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046243 restraints weight = 70101.518| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 5.22 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13304 Z= 0.206 Angle : 0.657 11.964 18434 Z= 0.345 Chirality : 0.041 0.213 2053 Planarity : 0.004 0.049 1998 Dihedral : 21.880 177.510 2716 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.26 % Allowed : 24.19 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.24), residues: 1298 helix: 1.44 (0.21), residues: 627 sheet: -0.94 (0.42), residues: 149 loop : -0.26 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.018 0.002 TYR A 61 PHE 0.014 0.001 PHE A1249 TRP 0.009 0.001 TRP A 765 HIS 0.006 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00447 (13304) covalent geometry : angle 0.65727 (18434) hydrogen bonds : bond 0.03784 ( 606) hydrogen bonds : angle 4.42053 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 732 MET cc_start: 0.9200 (tmm) cc_final: 0.8859 (tmm) REVERT: A 1014 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8207 (pp30) REVERT: A 1016 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: A 1224 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8549 (pp30) outliers start: 38 outliers final: 29 residues processed: 102 average time/residue: 0.1155 time to fit residues: 17.6871 Evaluate side-chains 104 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.069163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047393 restraints weight = 70191.918| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 5.15 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13304 Z= 0.168 Angle : 0.638 12.595 18434 Z= 0.331 Chirality : 0.040 0.204 2053 Planarity : 0.004 0.046 1998 Dihedral : 21.814 178.937 2716 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.92 % Allowed : 24.53 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.24), residues: 1298 helix: 1.54 (0.21), residues: 618 sheet: -0.85 (0.42), residues: 145 loop : -0.24 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.017 0.002 TYR A 61 PHE 0.014 0.001 PHE A 683 TRP 0.009 0.001 TRP A 765 HIS 0.005 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00373 (13304) covalent geometry : angle 0.63759 (18434) hydrogen bonds : bond 0.03549 ( 606) hydrogen bonds : angle 4.33303 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8380 (mm) REVERT: A 732 MET cc_start: 0.9216 (tmm) cc_final: 0.8878 (tmm) REVERT: A 916 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7907 (t80) REVERT: A 1016 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 1224 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8599 (pp30) outliers start: 34 outliers final: 30 residues processed: 102 average time/residue: 0.1081 time to fit residues: 16.8471 Evaluate side-chains 109 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 916 TYR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1224 GLN Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.068104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.046146 restraints weight = 71128.362| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 5.18 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13304 Z= 0.210 Angle : 0.661 13.615 18434 Z= 0.347 Chirality : 0.041 0.219 2053 Planarity : 0.004 0.049 1998 Dihedral : 21.885 177.516 2716 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.09 % Allowed : 24.44 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.24), residues: 1298 helix: 1.45 (0.21), residues: 619 sheet: -0.83 (0.43), residues: 145 loop : -0.21 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.028 0.002 TYR A 971 PHE 0.016 0.002 PHE A1249 TRP 0.009 0.001 TRP A 765 HIS 0.004 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00457 (13304) covalent geometry : angle 0.66098 (18434) hydrogen bonds : bond 0.03795 ( 606) hydrogen bonds : angle 4.42593 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 593 MET cc_start: 0.9363 (ptm) cc_final: 0.8527 (ppp) REVERT: A 1016 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7885 (mp0) outliers start: 36 outliers final: 30 residues processed: 101 average time/residue: 0.1078 time to fit residues: 16.4420 Evaluate side-chains 102 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1031 TYR Chi-restraints excluded: chain A residue 1049 PHE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.069601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047784 restraints weight = 68936.412| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 5.09 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13304 Z= 0.148 Angle : 0.652 13.286 18434 Z= 0.335 Chirality : 0.041 0.342 2053 Planarity : 0.004 0.050 1998 Dihedral : 21.796 179.144 2716 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.83 % Allowed : 24.53 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.24), residues: 1298 helix: 1.51 (0.21), residues: 624 sheet: -0.78 (0.43), residues: 145 loop : -0.18 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.018 0.001 TYR A 829 PHE 0.015 0.001 PHE A1249 TRP 0.011 0.001 TRP A 765 HIS 0.004 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00331 (13304) covalent geometry : angle 0.65237 (18434) hydrogen bonds : bond 0.03500 ( 606) hydrogen bonds : angle 4.29685 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.09 seconds wall clock time: 51 minutes 1.05 seconds (3061.05 seconds total)