Starting phenix.real_space_refine on Wed Jul 30 22:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfn_40445/07_2025/8sfn_40445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfn_40445/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfn_40445/07_2025/8sfn_40445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfn_40445/07_2025/8sfn_40445.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfn_40445/07_2025/8sfn_40445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfn_40445/07_2025/8sfn_40445.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.95, per 1000 atoms: 0.70 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: 3.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 5.27 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: 8.89 Time building geometry restraints manager: 4.56 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: 2.490 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 48.160 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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:4.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.057 0.003 TRP A 483 HIS 0.024 0.002 HIS A 479 PHE 0.029 0.002 PHE A 999 TYR 0.039 0.002 TYR A 971 ARG 0.014 0.001 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.15103 ( 606) hydrogen bonds : angle 7.07488 ( 1750) covalent geometry : bond 0.00536 (13304) covalent geometry : angle 1.22231 (18434) *********************** 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 : 1.284 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: 0.2526 time to fit residues: 39.1776 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 : 1.324 ------------------------------------------------------------------------------- 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 117 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 913 ASN A 929 GLN ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3687 r_free = 0.3687 target = 0.069188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046729 restraints weight = 69228.351| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 5.16 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13304 Z= 0.287 Angle : 0.734 10.305 18434 Z= 0.392 Chirality : 0.043 0.166 2053 Planarity : 0.005 0.099 1998 Dihedral : 22.119 175.115 2718 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.34 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1298 helix: 0.71 (0.20), residues: 625 sheet: -0.95 (0.45), residues: 134 loop : -0.54 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1258 HIS 0.011 0.002 HIS A 479 PHE 0.023 0.002 PHE A 198 TYR 0.023 0.002 TYR A 61 ARG 0.008 0.001 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.04644 ( 606) hydrogen bonds : angle 4.99574 ( 1750) covalent geometry : bond 0.00607 (13304) covalent geometry : angle 0.73446 (18434) *********************** 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 114 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 507 MET cc_start: 0.8977 (mmm) cc_final: 0.8678 (mmm) REVERT: A 624 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9053 (t) REVERT: A 1083 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8653 (m-10) outliers start: 39 outliers final: 17 residues processed: 103 average time/residue: 0.2954 time to fit residues: 45.5898 Evaluate side-chains 90 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 565 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 973 SER Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3697 r_free = 0.3697 target = 0.069708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.047422 restraints weight = 69761.700| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.20 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13304 Z= 0.183 Angle : 0.634 10.098 18434 Z= 0.338 Chirality : 0.040 0.164 2053 Planarity : 0.004 0.065 1998 Dihedral : 22.050 178.838 2716 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.92 % Allowed : 22.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1298 helix: 1.10 (0.21), residues: 626 sheet: -0.91 (0.44), residues: 141 loop : -0.40 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1298 HIS 0.008 0.001 HIS A 479 PHE 0.020 0.001 PHE A 999 TYR 0.019 0.002 TYR A 61 ARG 0.005 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 606) hydrogen bonds : angle 4.65244 ( 1750) covalent geometry : bond 0.00397 (13304) covalent geometry : angle 0.63446 (18434) *********************** 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 117 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8548 (tp30) cc_final: 0.8266 (tp30) REVERT: A 319 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 507 MET cc_start: 0.9069 (mmm) cc_final: 0.8814 (mmm) REVERT: A 732 MET cc_start: 0.9178 (tmm) cc_final: 0.8777 (tmm) REVERT: A 1238 ASN cc_start: 0.9614 (OUTLIER) cc_final: 0.8284 (m-40) outliers start: 34 outliers final: 18 residues processed: 108 average time/residue: 0.2515 time to fit residues: 40.9869 Evaluate side-chains 89 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 915 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1238 ASN 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 36 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.068498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046485 restraints weight = 69226.261| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 5.12 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13304 Z= 0.215 Angle : 0.643 10.441 18434 Z= 0.344 Chirality : 0.041 0.174 2053 Planarity : 0.004 0.048 1998 Dihedral : 22.066 177.422 2716 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.43 % Allowed : 22.13 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1298 helix: 1.27 (0.21), residues: 626 sheet: -1.02 (0.44), residues: 141 loop : -0.40 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 483 HIS 0.006 0.001 HIS A 479 PHE 0.017 0.001 PHE A 198 TYR 0.020 0.002 TYR A 829 ARG 0.004 0.000 ARG A 386 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 606) hydrogen bonds : angle 4.60274 ( 1750) covalent geometry : bond 0.00461 (13304) covalent geometry : angle 0.64301 (18434) *********************** 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 113 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 507 MET cc_start: 0.9217 (mmm) cc_final: 0.8977 (mmm) REVERT: A 624 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9053 (t) REVERT: A 1014 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 1016 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7723 (mp0) outliers start: 40 outliers final: 22 residues processed: 104 average time/residue: 0.2364 time to fit residues: 37.7858 Evaluate side-chains 92 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 142 VAL Chi-restraints excluded: chain A residue 149 VAL 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 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 684 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 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 1105 HIS Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.070131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047908 restraints weight = 68570.565| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.23 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2563 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= 0.137 Angle : 0.613 11.594 18434 Z= 0.321 Chirality : 0.039 0.196 2053 Planarity : 0.004 0.050 1998 Dihedral : 21.873 179.505 2716 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.00 % Allowed : 23.50 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1298 helix: 1.44 (0.21), residues: 623 sheet: -0.90 (0.42), residues: 142 loop : -0.28 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 483 HIS 0.006 0.001 HIS A 479 PHE 0.014 0.001 PHE A 198 TYR 0.018 0.001 TYR A 595 ARG 0.005 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 606) hydrogen bonds : angle 4.39399 ( 1750) covalent geometry : bond 0.00305 (13304) covalent geometry : angle 0.61280 (18434) *********************** 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 120 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8503 (tp30) cc_final: 0.8218 (tp30) REVERT: A 319 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 507 MET cc_start: 0.9228 (mmm) cc_final: 0.9019 (mmm) REVERT: A 732 MET cc_start: 0.9168 (tmm) cc_final: 0.8833 (tmm) REVERT: A 945 ASP cc_start: 0.8255 (m-30) cc_final: 0.7563 (p0) REVERT: A 1273 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8808 (mmtm) outliers start: 35 outliers final: 21 residues processed: 111 average time/residue: 0.2385 time to fit residues: 40.7913 Evaluate side-chains 99 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 262 LEU 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 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 915 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 PHE 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 1110 THR Chi-restraints excluded: chain A residue 1174 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1273 LYS 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 38 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.069030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047038 restraints weight = 70223.354| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 5.24 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13304 Z= 0.183 Angle : 0.630 11.937 18434 Z= 0.333 Chirality : 0.040 0.215 2053 Planarity : 0.004 0.052 1998 Dihedral : 21.862 177.761 2716 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.09 % Allowed : 24.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1298 helix: 1.50 (0.21), residues: 620 sheet: -0.83 (0.43), residues: 141 loop : -0.29 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1298 HIS 0.005 0.001 HIS A 479 PHE 0.015 0.001 PHE A 198 TYR 0.031 0.002 TYR A 971 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 606) hydrogen bonds : angle 4.41595 ( 1750) covalent geometry : bond 0.00398 (13304) covalent geometry : angle 0.63035 (18434) *********************** 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 111 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8551 (tp30) cc_final: 0.8226 (tp30) REVERT: A 319 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 732 MET cc_start: 0.9206 (tmm) cc_final: 0.8861 (tmm) REVERT: A 1016 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: A 1176 LEU cc_start: 0.9048 (tt) cc_final: 0.8812 (mm) outliers start: 36 outliers final: 22 residues processed: 101 average time/residue: 0.3157 time to fit residues: 47.8406 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 118 THR 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 319 ILE Chi-restraints excluded: chain A residue 325 SER 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 1049 PHE Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1301 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 107 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3718 r_free = 0.3718 target = 0.070610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048547 restraints weight = 68695.503| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.12 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13304 Z= 0.129 Angle : 0.624 12.578 18434 Z= 0.323 Chirality : 0.039 0.194 2053 Planarity : 0.004 0.063 1998 Dihedral : 21.758 179.922 2716 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.66 % Allowed : 24.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1298 helix: 1.56 (0.21), residues: 621 sheet: -0.41 (0.44), residues: 133 loop : -0.22 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1298 HIS 0.005 0.001 HIS A 479 PHE 0.014 0.001 PHE A 198 TYR 0.034 0.002 TYR A 971 ARG 0.013 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 606) hydrogen bonds : angle 4.32787 ( 1750) covalent geometry : bond 0.00288 (13304) covalent geometry : angle 0.62424 (18434) *********************** 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 110 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8518 (tp30) cc_final: 0.8156 (tp30) REVERT: A 319 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 732 MET cc_start: 0.9184 (tmm) cc_final: 0.8939 (tmm) REVERT: A 945 ASP cc_start: 0.8262 (m-30) cc_final: 0.7577 (p0) REVERT: A 1016 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7666 (mp0) outliers start: 31 outliers final: 23 residues processed: 104 average time/residue: 0.2777 time to fit residues: 44.8327 Evaluate side-chains 99 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 262 LEU 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 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 1049 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1248 CYS 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 28 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN A 913 ASN A 933 ASN A1014 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049104 restraints weight = 68984.296| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.23 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13304 Z= 0.126 Angle : 0.620 12.714 18434 Z= 0.319 Chirality : 0.039 0.187 2053 Planarity : 0.004 0.046 1998 Dihedral : 21.653 179.997 2716 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 24.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1298 helix: 1.53 (0.21), residues: 625 sheet: -0.23 (0.45), residues: 126 loop : -0.28 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 PHE 0.013 0.001 PHE A 198 TYR 0.018 0.001 TYR A 61 ARG 0.004 0.000 ARG A1174 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 606) hydrogen bonds : angle 4.25650 ( 1750) covalent geometry : bond 0.00282 (13304) covalent geometry : angle 0.61971 (18434) *********************** 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 106 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.8516 (tp30) cc_final: 0.8130 (tp30) REVERT: A 319 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 709 GLU cc_start: 0.9586 (OUTLIER) cc_final: 0.9226 (pt0) REVERT: A 732 MET cc_start: 0.9179 (tmm) cc_final: 0.8813 (tmm) REVERT: A 893 ASN cc_start: 0.9157 (m-40) cc_final: 0.8799 (m-40) REVERT: A 945 ASP cc_start: 0.8230 (m-30) cc_final: 0.7564 (p0) REVERT: A 1016 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8343 (mp0) outliers start: 29 outliers final: 20 residues processed: 100 average time/residue: 0.2340 time to fit residues: 36.2692 Evaluate side-chains 96 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 262 LEU 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 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 1049 PHE Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- 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 ** A 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN A 933 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.068742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046761 restraints weight = 70321.487| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.11 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13304 Z= 0.206 Angle : 0.656 12.679 18434 Z= 0.345 Chirality : 0.041 0.241 2053 Planarity : 0.004 0.045 1998 Dihedral : 21.802 176.228 2716 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1298 helix: 1.57 (0.21), residues: 617 sheet: -0.75 (0.43), residues: 145 loop : -0.27 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1298 HIS 0.004 0.001 HIS A1105 PHE 0.017 0.001 PHE A 683 TYR 0.019 0.002 TYR A 61 ARG 0.003 0.000 ARG A 797 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 606) hydrogen bonds : angle 4.39492 ( 1750) covalent geometry : bond 0.00447 (13304) covalent geometry : angle 0.65627 (18434) *********************** 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 103 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 593 MET cc_start: 0.9321 (ptm) cc_final: 0.8525 (ppp) REVERT: A 732 MET cc_start: 0.9212 (tmm) cc_final: 0.8853 (tmm) REVERT: A 916 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7998 (t80) REVERT: A 1016 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (mp0) outliers start: 33 outliers final: 28 residues processed: 94 average time/residue: 0.2486 time to fit residues: 35.9765 Evaluate side-chains 98 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 369 LYS 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 1105 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 104 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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** A 913 ASN A 933 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.070278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048364 restraints weight = 69209.096| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 5.26 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13304 Z= 0.130 Angle : 0.627 13.234 18434 Z= 0.324 Chirality : 0.040 0.242 2053 Planarity : 0.004 0.043 1998 Dihedral : 21.702 179.429 2716 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.57 % Allowed : 24.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.24), residues: 1298 helix: 1.55 (0.21), residues: 624 sheet: -0.61 (0.42), residues: 148 loop : -0.19 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 PHE 0.014 0.001 PHE A 198 TYR 0.017 0.001 TYR A 595 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 606) hydrogen bonds : angle 4.26394 ( 1750) covalent geometry : bond 0.00294 (13304) covalent geometry : angle 0.62660 (18434) ********************** 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 103 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 732 MET cc_start: 0.9196 (tmm) cc_final: 0.8837 (tmm) REVERT: A 1016 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8372 (mp0) outliers start: 30 outliers final: 23 residues processed: 96 average time/residue: 0.2727 time to fit residues: 40.0550 Evaluate side-chains 95 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 203 GLU 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 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 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 1248 CYS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.069910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047857 restraints weight = 70103.385| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 5.26 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13304 Z= 0.149 Angle : 0.633 13.367 18434 Z= 0.329 Chirality : 0.040 0.250 2053 Planarity : 0.004 0.044 1998 Dihedral : 21.691 178.122 2716 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 25.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1298 helix: 1.56 (0.21), residues: 625 sheet: -0.67 (0.41), residues: 152 loop : -0.15 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 765 HIS 0.004 0.001 HIS A 479 PHE 0.015 0.001 PHE A 999 TYR 0.017 0.001 TYR A 829 ARG 0.004 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 606) hydrogen bonds : angle 4.26429 ( 1750) covalent geometry : bond 0.00333 (13304) covalent geometry : angle 0.63319 (18434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.62 seconds wall clock time: 119 minutes 22.32 seconds (7162.32 seconds total)