Starting phenix.real_space_refine on Thu Jul 2 23:50:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgf_37219/07_2026/8kgf_37219.map" } resolution = 2.9 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= 0.001 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 6852 2.51 5 N 1799 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10872 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 10258 Classifications: {'peptide': 1261} Link IDs: {'PTRANS': 34, 'TRANS': 1226} Chain breaks: 5 Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 612 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.21 Number of scatterers: 10872 At special positions: 0 Unit cell: (100.64, 111.74, 132.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 29 15.00 Mg 2 11.99 O 2155 8.00 N 1799 7.00 C 6852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 541.5 milliseconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 54.6% alpha, 10.8% beta 8 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 38 through 69 removed outlier: 3.798A pdb=" N ASP A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 4.303A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 112 removed outlier: 3.913A pdb=" N LYS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.304A pdb=" N ILE A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.909A pdb=" N PHE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 173 removed outlier: 3.723A pdb=" N ASN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 removed outlier: 3.737A pdb=" N LEU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.563A pdb=" N MET A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 4.826A pdb=" N SER A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.570A pdb=" N SER A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 268 through 278 removed outlier: 3.577A pdb=" N LEU A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 4.708A pdb=" N VAL A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.515A pdb=" N VAL A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 375 through 389 removed outlier: 4.195A pdb=" N SER A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.781A pdb=" N GLU A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 4.154A pdb=" N GLU A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.551A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 removed outlier: 4.302A pdb=" N CYS A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 515 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 588 through 597 Proline residue: A 594 - end of helix Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 647 through 654 removed outlier: 4.306A pdb=" N ARG A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 677 removed outlier: 3.521A pdb=" N LYS A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 removed outlier: 3.749A pdb=" N LEU A 687 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE A 688 " --> pdb=" O THR A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 684 through 688' Processing helix chain 'A' and resid 690 through 694 removed outlier: 3.732A pdb=" N TYR A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 removed outlier: 3.914A pdb=" N PHE A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.599A pdb=" N ILE A 721 " --> pdb=" O PRO A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 749 through 758 removed outlier: 3.813A pdb=" N ILE A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.827A pdb=" N ASP A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 850 through 855 removed outlier: 4.090A pdb=" N VAL A 855 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 888 Processing helix chain 'A' and resid 923 through 927 removed outlier: 3.704A pdb=" N THR A 926 " --> pdb=" O THR A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 941 Processing helix chain 'A' and resid 946 through 976 removed outlier: 3.724A pdb=" N VAL A 950 " --> pdb=" O ASP A 946 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 963 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1013 removed outlier: 3.704A pdb=" N ASN A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.767A pdb=" N HIS A1076 " --> pdb=" O SER A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 Processing helix chain 'A' and resid 1167 through 1179 Processing helix chain 'A' and resid 1182 through 1186 removed outlier: 4.000A pdb=" N SER A1185 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.782A pdb=" N PHE A1196 " --> pdb=" O ILE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1242 through 1244 No H-bonds generated for 'chain 'A' and resid 1242 through 1244' Processing helix chain 'A' and resid 1251 through 1272 removed outlier: 3.701A pdb=" N GLY A1256 " --> pdb=" O ALA A1252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1257 " --> pdb=" O ASP A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1291 Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524 removed outlier: 4.483A pdb=" N PHE A 858 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 23 " --> pdb=" O HIS A 736 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 736 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 555 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 11.945A pdb=" N ALA A 546 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N TYR A 583 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 548 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 523 through 524 Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.602A pdb=" N ILE A 358 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA5, first strand: chain 'A' and resid 915 through 920 removed outlier: 3.523A pdb=" N GLU A 917 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU A 982 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N ARG A 898 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 979 " --> pdb=" O PHE A1052 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A1054 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 981 " --> pdb=" O VAL A1054 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1090 through 1095 removed outlier: 6.773A pdb=" N PHE A1090 " --> pdb=" O HIS A1107 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N HIS A1107 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A1092 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA8, first strand: chain 'A' and resid 1149 through 1151 Processing sheet with id=AA9, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 4.779A pdb=" N PHE A1239 " --> pdb=" O SER A1229 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A1231 " --> pdb=" O ILE A1237 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A1237 " --> pdb=" O ILE A1231 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2754 1.33 - 1.45: 2208 1.45 - 1.57: 6070 1.57 - 1.70: 55 1.70 - 1.82: 59 Bond restraints: 11146 Sorted by residual: bond pdb=" CA PRO A 353 " pdb=" C PRO A 353 " ideal model delta sigma weight residual 1.520 1.552 -0.031 9.50e-03 1.11e+04 1.08e+01 bond pdb=" CZ ARG A1242 " pdb=" NH2 ARG A1242 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.59e+00 bond pdb=" CZ ARG A 851 " pdb=" NH2 ARG A 851 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.44e+00 bond pdb=" CZ ARG A1272 " pdb=" NH2 ARG A1272 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.21e+00 bond pdb=" CZ ARG A1149 " pdb=" NH2 ARG A1149 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.03e+00 ... (remaining 11141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11094 1.55 - 3.10: 3326 3.10 - 4.64: 663 4.64 - 6.19: 49 6.19 - 7.74: 6 Bond angle restraints: 15138 Sorted by residual: angle pdb=" N VAL A 232 " pdb=" CA VAL A 232 " pdb=" C VAL A 232 " ideal model delta sigma weight residual 111.44 103.70 7.74 1.34e+00 5.57e-01 3.34e+01 angle pdb=" N PHE A 233 " pdb=" CA PHE A 233 " pdb=" C PHE A 233 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" N ILE A 450 " pdb=" CA ILE A 450 " pdb=" C ILE A 450 " ideal model delta sigma weight residual 113.20 108.41 4.79 9.60e-01 1.09e+00 2.49e+01 angle pdb=" N CYS A 197 " pdb=" CA CYS A 197 " pdb=" C CYS A 197 " ideal model delta sigma weight residual 112.38 107.08 5.30 1.22e+00 6.72e-01 1.88e+01 angle pdb=" C1' U G -17 " pdb=" N1 U G -17 " pdb=" C2 U G -17 " ideal model delta sigma weight residual 117.70 122.62 -4.92 1.20e+00 6.94e-01 1.68e+01 ... (remaining 15133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 6613 35.68 - 71.36: 119 71.36 - 107.04: 13 107.04 - 142.72: 0 142.72 - 178.40: 1 Dihedral angle restraints: 6746 sinusoidal: 3049 harmonic: 3697 Sorted by residual: dihedral pdb=" C5' A G 5 " pdb=" C4' A G 5 " pdb=" C3' A G 5 " pdb=" O3' A G 5 " ideal model delta sinusoidal sigma weight residual 147.00 89.04 57.96 1 8.00e+00 1.56e-02 7.04e+01 dihedral pdb=" O4' U G -7 " pdb=" C1' U G -7 " pdb=" N1 U G -7 " pdb=" C2 U G -7 " ideal model delta sinusoidal sigma weight residual -128.00 50.40 -178.40 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A G 5 " pdb=" C4' A G 5 " pdb=" C3' A G 5 " pdb=" C2' A G 5 " ideal model delta sinusoidal sigma weight residual 24.00 -31.42 55.42 1 8.00e+00 1.56e-02 6.49e+01 ... (remaining 6743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1189 0.075 - 0.150: 386 0.150 - 0.226: 87 0.226 - 0.301: 9 0.301 - 0.376: 3 Chirality restraints: 1674 Sorted by residual: chirality pdb=" CA TYR A1058 " pdb=" N TYR A1058 " pdb=" C TYR A1058 " pdb=" CB TYR A1058 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA HIS A1100 " pdb=" N HIS A1100 " pdb=" C HIS A1100 " pdb=" CB HIS A1100 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA THR A 597 " pdb=" N THR A 597 " pdb=" C THR A 597 " pdb=" CB THR A 597 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1671 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 470 " 0.103 2.00e-02 2.50e+03 5.90e-02 6.96e+01 pdb=" CG TYR A 470 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 470 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 470 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 470 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 470 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR A 470 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 470 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 694 " -0.103 2.00e-02 2.50e+03 5.69e-02 6.47e+01 pdb=" CG TYR A 694 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 694 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 694 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 694 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 694 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 694 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 694 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 95 " 0.105 2.00e-02 2.50e+03 5.68e-02 6.45e+01 pdb=" CG TYR A 95 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 95 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 95 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR A 95 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 95 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 95 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 95 " 0.087 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 19 2.55 - 3.14: 8327 3.14 - 3.72: 16023 3.72 - 4.31: 23251 4.31 - 4.90: 36717 Nonbonded interactions: 84337 Sorted by model distance: nonbonded pdb=" OP2 A G -4 " pdb="MG MG A1401 " model vdw 1.960 2.170 nonbonded pdb=" O LYS A 747 " pdb="MG MG A1401 " model vdw 1.999 2.170 nonbonded pdb=" O SER A 480 " pdb=" OG1 THR A 484 " model vdw 2.424 3.040 nonbonded pdb=" N HIS A1108 " pdb=" O ALA A1124 " model vdw 2.439 3.120 nonbonded pdb=" O2' U G 4 " pdb=" O5' A G 5 " model vdw 2.442 3.040 ... (remaining 84332 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.011 0.036 11146 Z= 0.645 Angle : 1.473 7.739 15138 Z= 1.007 Chirality : 0.076 0.376 1674 Planarity : 0.010 0.096 1828 Dihedral : 13.542 178.398 4368 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.44 % Allowed : 3.81 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.21), residues: 1249 helix: -1.16 (0.18), residues: 595 sheet: 0.41 (0.46), residues: 124 loop : -1.05 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1242 TYR 0.109 0.016 TYR A 583 PHE 0.055 0.008 PHE A 190 TRP 0.041 0.008 TRP A1284 HIS 0.010 0.002 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.01084 / 0.65 (11146) covalent geometry : angle 1.47270 / 1.01 (15138) hydrogen bonds : bond 0.21491 / 14.29 ( 498) hydrogen bonds : angle 7.61809 / 5.42 ( 1406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.428 Fit side-chains REVERT: A 122 LYS cc_start: 0.8260 (mmpt) cc_final: 0.7716 (mptt) REVERT: A 308 MET cc_start: 0.6517 (mmm) cc_final: 0.6199 (ptm) REVERT: A 344 LEU cc_start: 0.4783 (tp) cc_final: 0.4533 (mt) REVERT: A 422 ASP cc_start: 0.7375 (t0) cc_final: 0.6905 (p0) outliers start: 5 outliers final: 2 residues processed: 102 average time/residue: 0.7120 time to fit residues: 77.6679 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 384 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 941 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.109562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.073771 restraints weight = 25406.813| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.03 r_work: 0.3159 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11146 Z= 0.162 Angle : 0.617 6.682 15138 Z= 0.350 Chirality : 0.043 0.196 1674 Planarity : 0.004 0.037 1828 Dihedral : 12.151 178.773 1794 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.68 % Allowed : 7.53 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1249 helix: 0.41 (0.20), residues: 609 sheet: 0.56 (0.45), residues: 128 loop : -0.78 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 340 TYR 0.019 0.002 TYR A 95 PHE 0.027 0.002 PHE A 121 TRP 0.022 0.001 TRP A1284 HIS 0.008 0.002 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (11146) covalent geometry : angle 0.61714 / 0.35 (15138) hydrogen bonds : bond 0.06906 / 4.79 ( 498) hydrogen bonds : angle 5.28410 / 3.77 ( 1406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.430 Fit side-chains REVERT: A 122 LYS cc_start: 0.8291 (mmpt) cc_final: 0.7774 (mptt) REVERT: A 308 MET cc_start: 0.6751 (mmm) cc_final: 0.6299 (ptm) REVERT: A 900 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: A 1193 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8751 (mp) outliers start: 19 outliers final: 6 residues processed: 62 average time/residue: 0.5901 time to fit residues: 39.9330 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 1193 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.107272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071228 restraints weight = 25475.976| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.01 r_work: 0.3107 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11146 Z= 0.155 Angle : 0.525 8.213 15138 Z= 0.295 Chirality : 0.041 0.206 1674 Planarity : 0.004 0.045 1828 Dihedral : 11.897 177.550 1791 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 8.77 % Favored : 89.81 % 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 are not related in a simple way. whole: 0.28 (0.24), residues: 1249 helix: 0.98 (0.21), residues: 614 sheet: 0.40 (0.45), residues: 120 loop : -0.77 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 340 TYR 0.020 0.002 TYR A 430 PHE 0.018 0.002 PHE A 121 TRP 0.016 0.001 TRP A1284 HIS 0.007 0.002 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11146) covalent geometry : angle 0.52476 / 0.29 (15138) hydrogen bonds : bond 0.05258 / 3.60 ( 498) hydrogen bonds : angle 4.64921 / 3.30 ( 1406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.421 Fit side-chains REVERT: A 122 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7744 (mptt) REVERT: A 900 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7899 (mm-30) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 0.5334 time to fit residues: 33.4571 Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 89 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.107627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071438 restraints weight = 25506.315| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.01 r_work: 0.3114 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11146 Z= 0.118 Angle : 0.484 7.411 15138 Z= 0.268 Chirality : 0.039 0.201 1674 Planarity : 0.003 0.037 1828 Dihedral : 11.821 177.261 1791 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.68 % Allowed : 9.12 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1249 helix: 1.15 (0.21), residues: 616 sheet: 0.43 (0.44), residues: 130 loop : -0.84 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.019 0.001 TYR A 331 PHE 0.012 0.001 PHE A 523 TRP 0.017 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11146) covalent geometry : angle 0.48355 / 0.27 (15138) hydrogen bonds : bond 0.04572 / 3.14 ( 498) hydrogen bonds : angle 4.46036 / 3.17 ( 1406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.438 Fit side-chains REVERT: A 122 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7719 (mptt) REVERT: A 655 ASP cc_start: 0.7545 (t0) cc_final: 0.6570 (m-30) REVERT: A 900 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7832 (mm-30) outliers start: 19 outliers final: 5 residues processed: 57 average time/residue: 0.5204 time to fit residues: 32.7139 Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 924 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067770 restraints weight = 25614.484| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.02 r_work: 0.3041 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11146 Z= 0.254 Angle : 0.589 10.380 15138 Z= 0.322 Chirality : 0.043 0.213 1674 Planarity : 0.004 0.039 1828 Dihedral : 11.945 176.761 1791 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.68 % Allowed : 10.01 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1249 helix: 1.01 (0.21), residues: 606 sheet: 0.43 (0.44), residues: 130 loop : -0.94 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.027 0.002 TYR A 583 PHE 0.017 0.002 PHE A 7 TRP 0.013 0.001 TRP A1284 HIS 0.009 0.002 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (11146) covalent geometry : angle 0.58906 / 0.32 (15138) hydrogen bonds : bond 0.05784 / 3.95 ( 498) hydrogen bonds : angle 4.70860 / 3.33 ( 1406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.429 Fit side-chains REVERT: A 122 LYS cc_start: 0.8203 (mmpt) cc_final: 0.7733 (mptt) REVERT: A 655 ASP cc_start: 0.7500 (t0) cc_final: 0.7279 (t0) REVERT: A 890 ASP cc_start: 0.8424 (t0) cc_final: 0.8021 (p0) REVERT: A 900 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7926 (mm-30) outliers start: 19 outliers final: 8 residues processed: 58 average time/residue: 0.5347 time to fit residues: 34.1844 Evaluate side-chains 45 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.0040 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070147 restraints weight = 25602.428| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.01 r_work: 0.3082 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11146 Z= 0.104 Angle : 0.467 7.440 15138 Z= 0.259 Chirality : 0.039 0.202 1674 Planarity : 0.003 0.038 1828 Dihedral : 11.888 176.854 1791 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.06 % Allowed : 10.63 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1249 helix: 1.21 (0.21), residues: 614 sheet: 0.39 (0.44), residues: 132 loop : -0.86 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.017 0.001 TYR A 384 PHE 0.011 0.001 PHE A 523 TRP 0.024 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (11146) covalent geometry : angle 0.46725 / 0.26 (15138) hydrogen bonds : bond 0.04329 / 2.97 ( 498) hydrogen bonds : angle 4.37145 / 3.10 ( 1406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.428 Fit side-chains REVERT: A 122 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7730 (mptt) REVERT: A 890 ASP cc_start: 0.8439 (t0) cc_final: 0.7983 (p0) REVERT: A 900 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7858 (mm-30) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.6530 time to fit residues: 36.2211 Evaluate side-chains 44 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.103710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067677 restraints weight = 25537.348| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.02 r_work: 0.3038 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11146 Z= 0.236 Angle : 0.552 7.534 15138 Z= 0.302 Chirality : 0.042 0.210 1674 Planarity : 0.004 0.039 1828 Dihedral : 11.897 176.584 1791 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.77 % Allowed : 10.54 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1249 helix: 1.14 (0.21), residues: 607 sheet: 0.30 (0.43), residues: 137 loop : -0.94 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 882 TYR 0.025 0.002 TYR A 583 PHE 0.014 0.002 PHE A 523 TRP 0.012 0.001 TRP A1284 HIS 0.007 0.002 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (11146) covalent geometry : angle 0.55198 / 0.30 (15138) hydrogen bonds : bond 0.05410 / 3.69 ( 498) hydrogen bonds : angle 4.58080 / 3.25 ( 1406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.436 Fit side-chains REVERT: A 122 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7742 (mptt) REVERT: A 890 ASP cc_start: 0.8386 (t0) cc_final: 0.7978 (p0) REVERT: A 900 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7888 (mm-30) outliers start: 20 outliers final: 7 residues processed: 55 average time/residue: 0.5886 time to fit residues: 35.5212 Evaluate side-chains 46 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Chi-restraints excluded: chain A residue 924 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 461 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069835 restraints weight = 25645.667| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.03 r_work: 0.3085 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11146 Z= 0.108 Angle : 0.472 12.509 15138 Z= 0.257 Chirality : 0.039 0.259 1674 Planarity : 0.003 0.037 1828 Dihedral : 11.874 176.727 1791 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.33 % Allowed : 10.81 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1249 helix: 1.32 (0.21), residues: 610 sheet: 0.32 (0.43), residues: 139 loop : -0.85 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 944 TYR 0.020 0.001 TYR A 384 PHE 0.011 0.001 PHE A 523 TRP 0.024 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11146) covalent geometry : angle 0.47165 / 0.26 (15138) hydrogen bonds : bond 0.04260 / 2.92 ( 498) hydrogen bonds : angle 4.28030 / 3.04 ( 1406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8219 (mmpt) cc_final: 0.7755 (mptt) REVERT: A 608 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7398 (mm-40) REVERT: A 890 ASP cc_start: 0.8406 (t0) cc_final: 0.7936 (p0) REVERT: A 900 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7865 (mm-30) outliers start: 15 outliers final: 6 residues processed: 53 average time/residue: 0.6094 time to fit residues: 35.2388 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.104783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068842 restraints weight = 25375.129| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.99 r_work: 0.3065 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11146 Z= 0.159 Angle : 0.496 10.684 15138 Z= 0.269 Chirality : 0.040 0.200 1674 Planarity : 0.003 0.038 1828 Dihedral : 11.823 176.656 1791 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.42 % Allowed : 10.98 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1249 helix: 1.28 (0.21), residues: 615 sheet: 0.30 (0.43), residues: 139 loop : -0.85 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 142 TYR 0.020 0.001 TYR A 583 PHE 0.012 0.001 PHE A 523 TRP 0.016 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (11146) covalent geometry : angle 0.49587 / 0.27 (15138) hydrogen bonds : bond 0.04625 / 3.16 ( 498) hydrogen bonds : angle 4.33561 / 3.08 ( 1406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.246 Fit side-chains REVERT: A 122 LYS cc_start: 0.8226 (mmpt) cc_final: 0.7746 (mptt) REVERT: A 608 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7404 (mm-40) REVERT: A 890 ASP cc_start: 0.8414 (t0) cc_final: 0.7947 (p0) REVERT: A 900 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7885 (mm-30) outliers start: 16 outliers final: 6 residues processed: 50 average time/residue: 0.5397 time to fit residues: 29.2135 Evaluate side-chains 45 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.103770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.067976 restraints weight = 25562.975| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.02 r_work: 0.3044 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11146 Z= 0.218 Angle : 0.547 11.278 15138 Z= 0.296 Chirality : 0.042 0.200 1674 Planarity : 0.004 0.055 1828 Dihedral : 11.879 176.490 1791 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 11.07 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1249 helix: 1.19 (0.21), residues: 607 sheet: 0.29 (0.43), residues: 139 loop : -0.91 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 944 TYR 0.033 0.002 TYR A 430 PHE 0.014 0.002 PHE A 523 TRP 0.013 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (11146) covalent geometry : angle 0.54660 / 0.30 (15138) hydrogen bonds : bond 0.05154 / 3.52 ( 498) hydrogen bonds : angle 4.48832 / 3.19 ( 1406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.369 Fit side-chains REVERT: A 122 LYS cc_start: 0.8224 (mmpt) cc_final: 0.7747 (mptt) REVERT: A 608 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7368 (mm-40) REVERT: A 890 ASP cc_start: 0.8413 (t0) cc_final: 0.7934 (p0) REVERT: A 900 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7903 (mm-30) outliers start: 15 outliers final: 9 residues processed: 49 average time/residue: 0.4829 time to fit residues: 25.9496 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 856 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.1980 chunk 109 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.105205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069292 restraints weight = 25488.958| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.02 r_work: 0.3069 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11146 Z= 0.126 Angle : 0.484 9.961 15138 Z= 0.262 Chirality : 0.039 0.193 1674 Planarity : 0.003 0.037 1828 Dihedral : 11.854 176.602 1791 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.24 % Allowed : 11.25 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1249 helix: 1.39 (0.22), residues: 606 sheet: 0.37 (0.43), residues: 139 loop : -0.90 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 944 TYR 0.029 0.001 TYR A 430 PHE 0.015 0.001 PHE A 233 TRP 0.021 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (11146) covalent geometry : angle 0.48398 / 0.26 (15138) hydrogen bonds : bond 0.04364 / 2.99 ( 498) hydrogen bonds : angle 4.29767 / 3.06 ( 1406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.12 seconds wall clock time: 57 minutes 4.76 seconds (3424.76 seconds total)