Starting phenix.real_space_refine on Wed Aug 5 17:38:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgf_37219/08_2026/8kgf_37219_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgf_37219/08_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_37219/08_2026/8kgf_37219_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgf_37219/08_2026/8kgf_37219_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgf_37219/08_2026/8kgf_37219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgf_37219/08_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-2.2rc3-6140/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: 2.65, per 1000 atoms: 0.24 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: 0.92 Conformation dependent library (CDL) restraints added in 494.0 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: 1.22 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: 2.24 Time building geometry restraints manager: 1.22 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: 11046 1.55 - 3.10: 3373 3.10 - 4.64: 664 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: 1165 0.075 - 0.150: 413 0.150 - 0.226: 84 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: 2.200 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- 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= 0.647 Angle : 1.480 7.739 15138 Z= 1.015 Chirality : 0.077 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 1.48010 / 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 : 0.435 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: 0.7175 time to fit residues: 78.2370 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 : 0.409 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.109627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.073780 restraints weight = 25411.163| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.01 r_work: 0.3161 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11146 Z= 0.158 Angle : 0.619 6.881 15138 Z= 0.348 Chirality : 0.043 0.199 1674 Planarity : 0.004 0.036 1828 Dihedral : 12.094 179.054 1794 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.59 % Allowed : 7.71 % Favored : 90.70 % 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: -0.10 (0.23), residues: 1249 helix: 0.46 (0.20), residues: 608 sheet: 0.55 (0.45), residues: 128 loop : -0.77 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 340 TYR 0.017 0.002 TYR A 438 PHE 0.025 0.002 PHE A 121 TRP 0.025 0.001 TRP A1284 HIS 0.008 0.002 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (11146) covalent geometry : angle 0.61907 / 0.35 (15138) hydrogen bonds : bond 0.06487 / 4.51 ( 498) hydrogen bonds : angle 5.21244 / 3.72 ( 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: 18 poor density : 48 time to evaluate : 0.357 Fit side-chains REVERT: A 122 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7755 (mptt) REVERT: A 897 ASP cc_start: 0.8270 (t0) cc_final: 0.7373 (p0) REVERT: A 900 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: A 1193 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8754 (mp) outliers start: 18 outliers final: 6 residues processed: 62 average time/residue: 0.5726 time to fit residues: 38.7709 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 : 0.424 ------------------------------------------------------------------------------- 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: 0.3980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.109301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.073280 restraints weight = 25531.182| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.03 r_work: 0.3151 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11146 Z= 0.119 Angle : 0.498 7.240 15138 Z= 0.279 Chirality : 0.040 0.217 1674 Planarity : 0.004 0.047 1828 Dihedral : 11.824 177.934 1791 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.42 % Allowed : 8.59 % Favored : 89.99 % 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: 0.35 (0.23), residues: 1249 helix: 1.04 (0.21), residues: 615 sheet: 0.39 (0.45), residues: 120 loop : -0.74 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.025 0.002 TYR A 430 PHE 0.014 0.001 PHE A1038 TRP 0.015 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (11146) covalent geometry : angle 0.49788 / 0.28 (15138) hydrogen bonds : bond 0.04999 / 3.42 ( 498) hydrogen bonds : angle 4.55409 / 3.24 ( 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 59 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.419 Fit side-chains REVERT: A 122 LYS cc_start: 0.8226 (mmpt) cc_final: 0.7717 (mptt) REVERT: A 655 ASP cc_start: 0.7169 (t0) cc_final: 0.6287 (m-30) REVERT: A 900 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7824 (mm-30) outliers start: 16 outliers final: 2 residues processed: 56 average time/residue: 0.4855 time to fit residues: 30.0230 Evaluate side-chains 43 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 900 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 68 optimal weight: 0.0870 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.107135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070894 restraints weight = 25506.757| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.01 r_work: 0.3105 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11146 Z= 0.146 Angle : 0.513 8.892 15138 Z= 0.280 Chirality : 0.040 0.154 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.730 177.386 1791 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.68 % Allowed : 8.59 % Favored : 89.73 % 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: 0.42 (0.24), residues: 1249 helix: 1.17 (0.21), residues: 616 sheet: 0.38 (0.44), residues: 130 loop : -0.83 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 780 TYR 0.027 0.002 TYR A 430 PHE 0.013 0.002 PHE A 7 TRP 0.016 0.001 TRP A1284 HIS 0.007 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11146) covalent geometry : angle 0.51313 / 0.28 (15138) hydrogen bonds : bond 0.04815 / 3.31 ( 498) hydrogen bonds : angle 4.50104 / 3.19 ( 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 63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.291 Fit side-chains REVERT: A 122 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7722 (mptt) REVERT: A 890 ASP cc_start: 0.8415 (t0) cc_final: 0.8061 (p0) REVERT: A 900 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7845 (mm-30) outliers start: 19 outliers final: 6 residues processed: 59 average time/residue: 0.4732 time to fit residues: 30.6603 Evaluate side-chains 49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.107351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071208 restraints weight = 25374.729| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.99 r_work: 0.3112 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11146 Z= 0.116 Angle : 0.464 8.067 15138 Z= 0.255 Chirality : 0.039 0.179 1674 Planarity : 0.003 0.035 1828 Dihedral : 11.728 176.998 1791 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 9.39 % 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: 0.51 (0.24), residues: 1249 helix: 1.27 (0.21), residues: 615 sheet: 0.34 (0.44), residues: 132 loop : -0.79 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 142 TYR 0.018 0.001 TYR A 430 PHE 0.012 0.001 PHE A 523 TRP 0.018 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11146) covalent geometry : angle 0.46374 / 0.26 (15138) hydrogen bonds : bond 0.04304 / 2.94 ( 498) hydrogen bonds : angle 4.27590 / 3.04 ( 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 60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7730 (mptt) REVERT: A 655 ASP cc_start: 0.7447 (t0) cc_final: 0.6611 (m-30) REVERT: A 900 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7808 (mm-30) outliers start: 16 outliers final: 4 residues processed: 56 average time/residue: 0.5073 time to fit residues: 31.2458 Evaluate side-chains 45 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 40 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.106658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070433 restraints weight = 25558.805| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.00 r_work: 0.3084 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11146 Z= 0.136 Angle : 0.480 6.876 15138 Z= 0.263 Chirality : 0.039 0.145 1674 Planarity : 0.003 0.039 1828 Dihedral : 11.697 176.958 1791 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 9.92 % Favored : 88.75 % 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: 0.54 (0.24), residues: 1249 helix: 1.33 (0.21), residues: 615 sheet: 0.36 (0.44), residues: 132 loop : -0.82 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 142 TYR 0.024 0.001 TYR A 430 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 0.00311 / 0.14 (11146) covalent geometry : angle 0.47978 / 0.26 (15138) hydrogen bonds : bond 0.04403 / 3.00 ( 498) hydrogen bonds : angle 4.28525 / 3.04 ( 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: 15 poor density : 39 time to evaluate : 0.406 Fit side-chains REVERT: A 122 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7739 (mptt) REVERT: A 655 ASP cc_start: 0.7494 (t0) cc_final: 0.7282 (t0) REVERT: A 890 ASP cc_start: 0.8466 (t0) cc_final: 0.8043 (p0) REVERT: A 900 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7845 (mm-30) outliers start: 15 outliers final: 6 residues processed: 52 average time/residue: 0.6059 time to fit residues: 34.3416 Evaluate side-chains 43 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 924 VAL 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: 7.9990 chunk 107 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.105730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069538 restraints weight = 25413.515| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.99 r_work: 0.3072 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11146 Z= 0.153 Angle : 0.490 6.858 15138 Z= 0.268 Chirality : 0.040 0.146 1674 Planarity : 0.004 0.061 1828 Dihedral : 11.752 176.776 1791 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.51 % Allowed : 10.27 % Favored : 88.22 % 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: 1.35 (0.21), residues: 609 sheet: 0.22 (0.42), residues: 139 loop : -0.82 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 944 TYR 0.020 0.001 TYR A 583 PHE 0.012 0.001 PHE A 523 TRP 0.016 0.001 TRP A1284 HIS 0.005 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (11146) covalent geometry : angle 0.49016 / 0.27 (15138) hydrogen bonds : bond 0.04602 / 3.14 ( 498) hydrogen bonds : angle 4.29207 / 3.05 ( 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 57 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.350 Fit side-chains REVERT: A 122 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7756 (mptt) REVERT: A 890 ASP cc_start: 0.8471 (t0) cc_final: 0.7957 (p0) REVERT: A 900 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7873 (mm-30) outliers start: 17 outliers final: 7 residues processed: 55 average time/residue: 0.5604 time to fit residues: 33.9244 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 : 0.400 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.103893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067905 restraints weight = 25652.743| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.00 r_work: 0.3036 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11146 Z= 0.245 Angle : 0.586 15.750 15138 Z= 0.312 Chirality : 0.043 0.245 1674 Planarity : 0.004 0.037 1828 Dihedral : 11.893 176.636 1791 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.77 % Allowed : 10.45 % Favored : 87.78 % 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: 0.33 (0.24), residues: 1249 helix: 1.19 (0.21), residues: 601 sheet: 0.20 (0.42), residues: 139 loop : -0.93 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 944 TYR 0.026 0.002 TYR A 583 PHE 0.015 0.002 PHE A 523 TRP 0.011 0.001 TRP A1284 HIS 0.007 0.002 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.24 (11146) covalent geometry : angle 0.58552 / 0.31 (15138) hydrogen bonds : bond 0.05460 / 3.73 ( 498) hydrogen bonds : angle 4.52275 / 3.21 ( 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 60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.381 Fit side-chains REVERT: A 122 LYS cc_start: 0.8223 (mmpt) cc_final: 0.7734 (mptt) REVERT: A 890 ASP cc_start: 0.8428 (t0) cc_final: 0.8003 (p0) REVERT: A 900 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7883 (mm-30) outliers start: 20 outliers final: 7 residues processed: 56 average time/residue: 0.5390 time to fit residues: 33.0884 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 : 0.424 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.105797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.069857 restraints weight = 25309.527| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.00 r_work: 0.3081 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11146 Z= 0.117 Angle : 0.484 10.023 15138 Z= 0.263 Chirality : 0.039 0.138 1674 Planarity : 0.003 0.036 1828 Dihedral : 11.823 176.879 1791 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.89 % Allowed : 11.34 % Favored : 87.78 % 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: 0.57 (0.24), residues: 1249 helix: 1.42 (0.21), residues: 605 sheet: 0.29 (0.43), residues: 139 loop : -0.86 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 944 TYR 0.018 0.001 TYR A 583 PHE 0.011 0.001 PHE A 523 TRP 0.022 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11146) covalent geometry : angle 0.48357 / 0.26 (15138) hydrogen bonds : bond 0.04326 / 2.97 ( 498) hydrogen bonds : angle 4.23271 / 3.01 ( 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 53 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.330 Fit side-chains REVERT: A 122 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7730 (mptt) REVERT: A 890 ASP cc_start: 0.8450 (t0) cc_final: 0.7925 (p0) REVERT: A 900 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7841 (mm-30) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.5317 time to fit residues: 29.3670 Evaluate side-chains 45 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.106132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070063 restraints weight = 25486.447| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.03 r_work: 0.3075 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3471 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= 0.119 Angle : 0.494 10.633 15138 Z= 0.264 Chirality : 0.039 0.142 1674 Planarity : 0.003 0.035 1828 Dihedral : 11.739 176.934 1791 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.06 % Allowed : 11.25 % 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: 0.66 (0.24), residues: 1249 helix: 1.53 (0.22), residues: 602 sheet: 0.32 (0.43), residues: 139 loop : -0.85 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 944 TYR 0.025 0.001 TYR A 384 PHE 0.011 0.001 PHE A 523 TRP 0.019 0.001 TRP A1284 HIS 0.006 0.001 HIS A1259 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11146) covalent geometry : angle 0.49446 / 0.26 (15138) hydrogen bonds : bond 0.04220 / 2.88 ( 498) hydrogen bonds : angle 4.18592 / 2.98 ( 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 49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7750 (mptt) REVERT: A 890 ASP cc_start: 0.8471 (t0) cc_final: 0.7942 (p0) REVERT: A 900 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7860 (mm-30) outliers start: 12 outliers final: 8 residues processed: 45 average time/residue: 0.6056 time to fit residues: 29.8669 Evaluate side-chains 46 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR 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 485 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.105244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069185 restraints weight = 25489.294| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.02 r_work: 0.3064 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11146 Z= 0.157 Angle : 0.509 10.373 15138 Z= 0.273 Chirality : 0.040 0.146 1674 Planarity : 0.003 0.035 1828 Dihedral : 11.745 176.793 1791 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.15 % Allowed : 11.34 % 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: 0.62 (0.24), residues: 1249 helix: 1.50 (0.21), residues: 601 sheet: 0.29 (0.43), residues: 139 loop : -0.86 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 944 TYR 0.035 0.001 TYR A 430 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 0.00369 / 0.16 (11146) covalent geometry : angle 0.50907 / 0.27 (15138) hydrogen bonds : bond 0.04557 / 3.11 ( 498) hydrogen bonds : angle 4.24879 / 3.02 ( 1406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3178.83 seconds wall clock time: 55 minutes 0.53 seconds (3300.53 seconds total)