Starting phenix.real_space_refine on Thu Jul 2 19:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe7_70389/07_2026/9oe7_70389.cif" } resolution = 3.95 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= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5907 2.51 5 N 1560 2.21 5 O 1718 1.98 5 H 158 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9276 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 27, 'TRANS': 1148} Chain breaks: 2 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {' MG': 2, 'AGS': 2, 'R1Q': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.88, per 1000 atoms: 0.20 Number of scatterers: 9400 At special positions: 0 Unit cell: (70.55, 113.71, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1718 8.00 N 1560 7.00 C 5907 6.00 H 158 1.00 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: 0.91 Conformation dependent library (CDL) restraints added in 226.6 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 70.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.682A pdb=" N PHE A 45 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 96 Proline residue: A 71 - end of helix removed outlier: 4.419A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 163 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 189 removed outlier: 5.146A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 4.078A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 252 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 274 through 328 removed outlier: 3.858A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 353 Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.504A pdb=" N ILE A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.613A pdb=" N GLN A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 467 through 473 removed outlier: 4.668A pdb=" N ARG A 472 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU A 473 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.648A pdb=" N ILE A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 550 removed outlier: 3.504A pdb=" N LYS A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.613A pdb=" N ILE A 573 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 576 " --> pdb=" O THR A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.745A pdb=" N PHE A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.882A pdb=" N VAL A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 738 removed outlier: 3.807A pdb=" N MET A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 4.619A pdb=" N ALA A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 729 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE A 734 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 735 " --> pdb=" O PHE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 797 removed outlier: 3.796A pdb=" N PHE A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 807 removed outlier: 3.574A pdb=" N ASP A 804 " --> pdb=" O TRP A 801 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 805 " --> pdb=" O TYR A 802 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS A 806 " --> pdb=" O ASP A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.896A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.997A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 853 through 880 removed outlier: 4.017A pdb=" N LEU A 857 " --> pdb=" O TRP A 853 " (cutoff:3.500A) Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 881 through 901 removed outlier: 5.460A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 912 through 964 removed outlier: 3.519A pdb=" N SER A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Proline residue: A 925 - end of helix removed outlier: 4.806A pdb=" N ILE A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR A 948 " --> pdb=" O GLN A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 991 removed outlier: 4.158A pdb=" N ALA A 983 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A 991 " --> pdb=" O GLY A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1075 through 1081 removed outlier: 3.776A pdb=" N GLN A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1081 " --> pdb=" O THR A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 3.794A pdb=" N GLN A1110 " --> pdb=" O TRP A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1139 through 1150 removed outlier: 3.589A pdb=" N ILE A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1157 removed outlier: 3.722A pdb=" N GLU A1157 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1165 Processing helix chain 'A' and resid 1175 through 1190 removed outlier: 3.722A pdb=" N ALA A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.511A pdb=" N ILE A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 removed outlier: 3.695A pdb=" N GLN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1232 through 1237' Processing helix chain 'A' and resid 1254 through 1262 Processing helix chain 'A' and resid 1262 through 1273 removed outlier: 3.757A pdb=" N THR A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421 removed outlier: 7.148A pdb=" N LEU A 420 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS A 400 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN A 401 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER A 455 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 430 through 432 removed outlier: 6.458A pdb=" N ILE A 603 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.262A pdb=" N GLY A 476 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1038 through 1040 removed outlier: 4.781A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1112 through 1114 removed outlier: 6.226A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP A1198 " --> pdb=" O GLY A1112 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A1114 " --> pdb=" O ASP A1198 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A1228 " --> pdb=" O LEU A1195 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A1197 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1093 through 1094 596 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 158 1.06 - 1.28: 1517 1.28 - 1.51: 3904 1.51 - 1.73: 3899 1.73 - 1.95: 88 Bond restraints: 9566 Sorted by residual: bond pdb=" C50 R1Q A1305 " pdb=" N49 R1Q A1305 " ideal model delta sigma weight residual 1.468 1.733 -0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C01 R1Q A1305 " pdb=" C60 R1Q A1305 " ideal model delta sigma weight residual 1.540 1.287 0.253 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C56 R1Q A1305 " pdb=" C60 R1Q A1305 " ideal model delta sigma weight residual 1.536 1.300 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C52 R1Q A1305 " pdb=" C53 R1Q A1305 " ideal model delta sigma weight residual 1.563 1.373 0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C31 R1Q A1305 " pdb=" C52 R1Q A1305 " ideal model delta sigma weight residual 1.545 1.374 0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 9561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.03: 13082 12.03 - 24.07: 18 24.07 - 36.10: 4 36.10 - 48.14: 2 48.14 - 60.17: 1 Bond angle restraints: 13107 Sorted by residual: angle pdb=" C48 R1Q A1305 " pdb=" N49 R1Q A1305 " pdb=" C50 R1Q A1305 " ideal model delta sigma weight residual 110.62 50.45 60.17 3.00e+00 1.11e-01 4.02e+02 angle pdb=" C02 R1Q A1305 " pdb=" N03 R1Q A1305 " pdb=" C55 R1Q A1305 " ideal model delta sigma weight residual 114.29 69.12 45.17 3.00e+00 1.11e-01 2.27e+02 angle pdb=" C58 R1Q A1305 " pdb=" C56 R1Q A1305 " pdb=" C60 R1Q A1305 " ideal model delta sigma weight residual 111.61 155.97 -44.36 3.00e+00 1.11e-01 2.19e+02 angle pdb=" C55 R1Q A1305 " pdb=" C56 R1Q A1305 " pdb=" C60 R1Q A1305 " ideal model delta sigma weight residual 109.13 81.76 27.37 3.00e+00 1.11e-01 8.32e+01 angle pdb=" C04 R1Q A1305 " pdb=" N03 R1Q A1305 " pdb=" C55 R1Q A1305 " ideal model delta sigma weight residual 120.58 93.50 27.08 3.00e+00 1.11e-01 8.15e+01 ... (remaining 13102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 5405 32.85 - 65.71: 345 65.71 - 98.56: 41 98.56 - 131.41: 9 131.41 - 164.26: 5 Dihedral angle restraints: 5805 sinusoidal: 2423 harmonic: 3382 Sorted by residual: dihedral pdb=" CA MET A 38 " pdb=" C MET A 38 " pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ALA A 826 " pdb=" C ALA A 826 " pdb=" N THR A 827 " pdb=" CA THR A 827 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" O1B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 138.55 -25.71 164.26 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 1463 0.203 - 0.405: 5 0.405 - 0.608: 1 0.608 - 0.810: 1 0.810 - 1.013: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" C43 R1Q A1305 " pdb=" C38 R1Q A1305 " pdb=" C46 R1Q A1305 " pdb=" C53 R1Q A1305 " both_signs ideal model delta sigma weight residual False 2.66 1.65 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C52 R1Q A1305 " pdb=" C22 R1Q A1305 " pdb=" C31 R1Q A1305 " pdb=" C51 R1Q A1305 " both_signs ideal model delta sigma weight residual False 3.01 2.04 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" C53 R1Q A1305 " pdb=" C43 R1Q A1305 " pdb=" C52 R1Q A1305 " pdb=" N49 R1Q A1305 " both_signs ideal model delta sigma weight residual False -2.24 -3.01 0.77 2.00e-01 2.50e+01 1.47e+01 ... (remaining 1469 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 R1Q A1305 " -0.012 2.00e-02 2.50e+03 7.86e-02 1.55e+02 pdb=" C20 R1Q A1305 " -0.015 2.00e-02 2.50e+03 pdb=" C21 R1Q A1305 " 0.018 2.00e-02 2.50e+03 pdb=" C22 R1Q A1305 " 0.027 2.00e-02 2.50e+03 pdb=" C23 R1Q A1305 " 0.181 2.00e-02 2.50e+03 pdb=" C24 R1Q A1305 " -0.146 2.00e-02 2.50e+03 pdb=" C25 R1Q A1305 " 0.034 2.00e-02 2.50e+03 pdb=" C52 R1Q A1305 " -0.064 2.00e-02 2.50e+03 pdb=" N28 R1Q A1305 " -0.030 2.00e-02 2.50e+03 pdb=" O26 R1Q A1305 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1166 " -0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" CD GLN A1166 " 0.082 2.00e-02 2.50e+03 pdb=" OE1 GLN A1166 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN A1166 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 R1Q A1305 " -0.000 2.00e-02 2.50e+03 1.71e-02 8.03e+00 pdb=" C06 R1Q A1305 " -0.001 2.00e-02 2.50e+03 pdb=" C07 R1Q A1305 " 0.046 2.00e-02 2.50e+03 pdb=" C09 R1Q A1305 " 0.001 2.00e-02 2.50e+03 pdb=" C10 R1Q A1305 " 0.000 2.00e-02 2.50e+03 pdb=" C11 R1Q A1305 " 0.001 2.00e-02 2.50e+03 pdb=" C12 R1Q A1305 " -0.010 2.00e-02 2.50e+03 pdb=" C13 R1Q A1305 " -0.001 2.00e-02 2.50e+03 pdb=" C14 R1Q A1305 " -0.000 2.00e-02 2.50e+03 pdb=" C15 R1Q A1305 " -0.031 2.00e-02 2.50e+03 pdb=" N08 R1Q A1305 " -0.005 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.48: 252 2.48 - 3.01: 6560 3.01 - 3.54: 13218 3.54 - 4.07: 16741 4.07 - 4.60: 24994 Nonbonded interactions: 61765 Sorted by model distance: nonbonded pdb=" O HIS A 880 " pdb=" HD1 HIS A 880 " model vdw 1.951 2.450 nonbonded pdb=" O GLY A 113 " pdb=" HG1 THR A 117 " model vdw 1.965 2.450 nonbonded pdb=" OD1 ASN A 109 " pdb=" H LEU A 112 " model vdw 2.008 2.450 nonbonded pdb=" HB2 GLN A 873 " pdb=" HG3 GLN A 873 " model vdw 2.116 1.952 nonbonded pdb=" H ILE A 110 " pdb="HG23 ILE A 110 " model vdw 2.121 2.270 ... (remaining 61760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.110 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.840 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 : 0.008 0.265 9408 Z= 0.420 Angle : 1.373 60.173 12746 Z= 0.538 Chirality : 0.060 1.013 1472 Planarity : 0.004 0.079 1603 Dihedral : 21.658 164.262 3588 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.00 % Allowed : 26.43 % Favored : 69.57 % 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: -0.59 (0.25), residues: 1170 helix: 0.47 (0.18), residues: 756 sheet: -1.82 (0.62), residues: 71 loop : -1.89 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 364 TYR 0.015 0.001 TYR A 185 PHE 0.015 0.001 PHE A 973 TRP 0.009 0.001 TRP A 707 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.42 ( 9408) covalent geometry : angle 1.37259 / 0.54 (12746) hydrogen bonds : bond 0.11530 / 7.35 ( 596) hydrogen bonds : angle 5.79768 / 4.09 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 54 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8855 (ttm) cc_final: 0.8514 (tmm) REVERT: A 57 MET cc_start: 0.9467 (mmm) cc_final: 0.9215 (mmm) REVERT: A 197 MET cc_start: 0.9473 (mtm) cc_final: 0.9179 (mmm) REVERT: A 241 MET cc_start: 0.9532 (ttm) cc_final: 0.9328 (mtm) REVERT: A 304 MET cc_start: 0.9723 (mmp) cc_final: 0.9209 (mmp) REVERT: A 310 MET cc_start: 0.9454 (mmm) cc_final: 0.9122 (mmm) REVERT: A 413 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9131 (mmmt) REVERT: A 543 ARG cc_start: 0.9481 (OUTLIER) cc_final: 0.8505 (ttp-170) REVERT: A 700 LEU cc_start: 0.9730 (tp) cc_final: 0.9517 (mm) REVERT: A 730 ILE cc_start: 0.9695 (OUTLIER) cc_final: 0.9375 (tp) REVERT: A 784 MET cc_start: 0.9138 (tmm) cc_final: 0.8606 (tmm) REVERT: A 816 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9143 (tp) REVERT: A 866 MET cc_start: 0.9104 (tmm) cc_final: 0.8840 (ppp) REVERT: A 957 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8518 (t80) REVERT: A 1091 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8572 (tmt-80) outliers start: 39 outliers final: 32 residues processed: 86 average time/residue: 0.0761 time to fit residues: 9.8213 Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1093 MET Chi-restraints excluded: chain A residue 1114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN A1032 ASN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 GLN A1180 GLN A1257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.027270 restraints weight = 82121.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.028236 restraints weight = 48516.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028903 restraints weight = 34863.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.029357 restraints weight = 27963.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029624 restraints weight = 24102.844| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9408 Z= 0.215 Angle : 0.620 8.983 12746 Z= 0.316 Chirality : 0.037 0.356 1472 Planarity : 0.004 0.039 1603 Dihedral : 17.145 156.878 1534 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 43.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.53 % Allowed : 25.92 % Favored : 68.55 % 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: 0.32 (0.25), residues: 1170 helix: 1.26 (0.18), residues: 773 sheet: -1.34 (0.66), residues: 70 loop : -1.97 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 281 TYR 0.007 0.001 TYR A 185 PHE 0.016 0.001 PHE A 404 TRP 0.007 0.001 TRP A 801 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 ( 9408) covalent geometry : angle 0.62027 / 0.32 (12746) hydrogen bonds : bond 0.04836 / 3.05 ( 596) hydrogen bonds : angle 4.76330 / 3.41 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 58 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.9647 (mmp) cc_final: 0.9226 (mmp) REVERT: A 310 MET cc_start: 0.9440 (mmm) cc_final: 0.9111 (mmm) REVERT: A 344 LEU cc_start: 0.9690 (tp) cc_final: 0.9473 (tt) REVERT: A 413 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9084 (mmtt) REVERT: A 621 MET cc_start: 0.8619 (mmm) cc_final: 0.8360 (mmm) REVERT: A 738 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.9007 (t80) REVERT: A 784 MET cc_start: 0.9186 (tmm) cc_final: 0.8675 (tmm) REVERT: A 836 GLN cc_start: 0.9599 (OUTLIER) cc_final: 0.9229 (mm-40) REVERT: A 957 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8594 (t80) REVERT: A 1082 GLU cc_start: 0.9244 (tt0) cc_final: 0.8961 (tt0) REVERT: A 1091 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8494 (tmt-80) REVERT: A 1207 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8879 (pm20) outliers start: 54 outliers final: 34 residues processed: 107 average time/residue: 0.0680 time to fit residues: 10.9864 Evaluate side-chains 95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027980 restraints weight = 79057.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.028978 restraints weight = 46498.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.029655 restraints weight = 33333.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.030122 restraints weight = 26723.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.030441 restraints weight = 22975.927| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9408 Z= 0.116 Angle : 0.472 7.029 12746 Z= 0.243 Chirality : 0.035 0.233 1472 Planarity : 0.003 0.030 1603 Dihedral : 15.694 157.786 1494 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 43.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.51 % Allowed : 26.74 % Favored : 68.75 % 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: 1.05 (0.26), residues: 1170 helix: 1.87 (0.19), residues: 772 sheet: -1.34 (0.62), residues: 82 loop : -1.75 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 796 TYR 0.005 0.001 TYR A 996 PHE 0.009 0.001 PHE A 955 TRP 0.005 0.001 TRP A 167 HIS 0.004 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 ( 9408) covalent geometry : angle 0.47204 / 0.24 (12746) hydrogen bonds : bond 0.04389 / 2.76 ( 596) hydrogen bonds : angle 4.21435 / 3.01 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9619 (mmp) cc_final: 0.9186 (mmp) REVERT: A 310 MET cc_start: 0.9402 (mmm) cc_final: 0.9103 (mmm) REVERT: A 344 LEU cc_start: 0.9670 (tp) cc_final: 0.9450 (tt) REVERT: A 621 MET cc_start: 0.8710 (mmm) cc_final: 0.8389 (mmm) REVERT: A 784 MET cc_start: 0.9179 (tmm) cc_final: 0.8643 (tmm) REVERT: A 957 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8565 (t80) REVERT: A 1091 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8334 (tmt-80) outliers start: 44 outliers final: 33 residues processed: 96 average time/residue: 0.0681 time to fit residues: 10.1840 Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 0.0070 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029033 restraints weight = 79215.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030068 restraints weight = 46422.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.030776 restraints weight = 33104.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031257 restraints weight = 26404.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.031575 restraints weight = 22648.449| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9408 Z= 0.089 Angle : 0.460 11.279 12746 Z= 0.228 Chirality : 0.035 0.239 1472 Planarity : 0.002 0.038 1603 Dihedral : 14.950 160.294 1488 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 42.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.30 % Allowed : 26.23 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1170 helix: 2.24 (0.19), residues: 775 sheet: -1.10 (0.63), residues: 82 loop : -1.57 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1083 TYR 0.009 0.001 TYR A 135 PHE 0.006 0.001 PHE A 757 TRP 0.004 0.001 TRP A 320 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.09 ( 9408) covalent geometry : angle 0.45994 / 0.23 (12746) hydrogen bonds : bond 0.03926 / 2.47 ( 596) hydrogen bonds : angle 3.81439 / 2.72 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9611 (mmp) cc_final: 0.9159 (mmp) REVERT: A 310 MET cc_start: 0.9383 (mmm) cc_final: 0.9068 (mmm) REVERT: A 344 LEU cc_start: 0.9654 (tp) cc_final: 0.9298 (tt) REVERT: A 348 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: A 409 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8927 (mtm110) REVERT: A 621 MET cc_start: 0.8842 (mmm) cc_final: 0.8495 (mmm) REVERT: A 784 MET cc_start: 0.9200 (tmm) cc_final: 0.8666 (tmm) REVERT: A 957 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8512 (t80) REVERT: A 1091 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8187 (tmt-80) outliers start: 42 outliers final: 28 residues processed: 95 average time/residue: 0.0764 time to fit residues: 10.9435 Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.035580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.026580 restraints weight = 85068.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027531 restraints weight = 50482.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.028181 restraints weight = 36386.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.028624 restraints weight = 29239.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028924 restraints weight = 25191.318| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9408 Z= 0.318 Angle : 0.688 8.381 12746 Z= 0.361 Chirality : 0.038 0.241 1472 Planarity : 0.004 0.039 1603 Dihedral : 14.749 158.795 1483 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 64.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.25 % Allowed : 26.02 % Favored : 67.73 % 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: 0.87 (0.25), residues: 1170 helix: 1.72 (0.19), residues: 776 sheet: -1.17 (0.63), residues: 82 loop : -1.89 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 910 TYR 0.011 0.002 TYR A 996 PHE 0.030 0.002 PHE A 738 TRP 0.009 0.001 TRP A 960 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.32 ( 9408) covalent geometry : angle 0.68772 / 0.36 (12746) hydrogen bonds : bond 0.04401 / 2.75 ( 596) hydrogen bonds : angle 4.60086 / 3.28 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 52 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9605 (mmp) cc_final: 0.9210 (mmp) REVERT: A 306 PHE cc_start: 0.9621 (OUTLIER) cc_final: 0.9207 (t80) REVERT: A 310 MET cc_start: 0.9455 (mmm) cc_final: 0.8969 (mmm) REVERT: A 344 LEU cc_start: 0.9659 (tp) cc_final: 0.9316 (tt) REVERT: A 348 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: A 413 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9117 (mmtt) REVERT: A 550 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9132 (pp) REVERT: A 621 MET cc_start: 0.9062 (mmm) cc_final: 0.8699 (mmm) REVERT: A 784 MET cc_start: 0.9222 (tmm) cc_final: 0.8718 (tmm) REVERT: A 836 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.9103 (tp40) REVERT: A 957 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8600 (t80) REVERT: A 1007 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9477 (mm) outliers start: 61 outliers final: 43 residues processed: 104 average time/residue: 0.0702 time to fit residues: 10.9813 Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 52 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1194 VAL Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 617 HIS ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.026587 restraints weight = 83152.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.027535 restraints weight = 49785.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028192 restraints weight = 35883.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.028620 restraints weight = 28759.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.028937 restraints weight = 24837.825| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9408 Z= 0.209 Angle : 0.556 7.335 12746 Z= 0.290 Chirality : 0.036 0.260 1472 Planarity : 0.003 0.031 1603 Dihedral : 14.369 164.013 1479 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 62.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.94 % Allowed : 26.23 % Favored : 67.83 % 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: 0.90 (0.25), residues: 1170 helix: 1.76 (0.19), residues: 775 sheet: -1.14 (0.63), residues: 82 loop : -1.92 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.008 0.001 TYR A 996 PHE 0.018 0.001 PHE A 738 TRP 0.007 0.001 TRP A 960 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.21 ( 9408) covalent geometry : angle 0.55639 / 0.29 (12746) hydrogen bonds : bond 0.04194 / 2.63 ( 596) hydrogen bonds : angle 4.37063 / 3.12 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 55 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9438 (p0) cc_final: 0.9217 (p0) REVERT: A 194 LYS cc_start: 0.9545 (OUTLIER) cc_final: 0.8983 (mmmm) REVERT: A 304 MET cc_start: 0.9590 (mmp) cc_final: 0.9180 (mmp) REVERT: A 306 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.9184 (t80) REVERT: A 310 MET cc_start: 0.9426 (mmm) cc_final: 0.8957 (mmm) REVERT: A 344 LEU cc_start: 0.9665 (tp) cc_final: 0.9323 (tt) REVERT: A 348 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: A 413 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9075 (mptt) REVERT: A 621 MET cc_start: 0.9183 (mmm) cc_final: 0.8736 (mmm) REVERT: A 784 MET cc_start: 0.9220 (tmm) cc_final: 0.8710 (tmm) REVERT: A 957 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8569 (t80) REVERT: A 1007 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9439 (mm) REVERT: A 1162 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8682 (mtm-85) outliers start: 58 outliers final: 45 residues processed: 103 average time/residue: 0.0637 time to fit residues: 9.9786 Evaluate side-chains 108 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 56 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027552 restraints weight = 80858.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028554 restraints weight = 48148.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029223 restraints weight = 34378.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029691 restraints weight = 27522.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029993 restraints weight = 23579.776| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9408 Z= 0.102 Angle : 0.471 7.524 12746 Z= 0.239 Chirality : 0.035 0.254 1472 Planarity : 0.003 0.029 1603 Dihedral : 13.995 169.038 1479 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 54.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.89 % Allowed : 28.48 % Favored : 67.62 % 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: 1.51 (0.26), residues: 1170 helix: 2.21 (0.19), residues: 776 sheet: -0.87 (0.63), residues: 81 loop : -1.68 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1091 TYR 0.005 0.001 TYR A 627 PHE 0.013 0.001 PHE A 140 TRP 0.004 0.001 TRP A 960 HIS 0.015 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 ( 9408) covalent geometry : angle 0.47108 / 0.24 (12746) hydrogen bonds : bond 0.03912 / 2.46 ( 596) hydrogen bonds : angle 3.95597 / 2.83 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9480 (p0) cc_final: 0.9249 (p0) REVERT: A 194 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.8904 (mmmm) REVERT: A 304 MET cc_start: 0.9599 (mmp) cc_final: 0.9149 (mmp) REVERT: A 306 PHE cc_start: 0.9608 (OUTLIER) cc_final: 0.9163 (t80) REVERT: A 310 MET cc_start: 0.9403 (mmm) cc_final: 0.8897 (mmm) REVERT: A 344 LEU cc_start: 0.9647 (tp) cc_final: 0.9314 (tt) REVERT: A 348 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: A 621 MET cc_start: 0.9068 (mmm) cc_final: 0.8702 (mmm) REVERT: A 784 MET cc_start: 0.9226 (tmm) cc_final: 0.8724 (tmm) REVERT: A 957 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8519 (t80) REVERT: A 1007 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9406 (mm) outliers start: 38 outliers final: 30 residues processed: 89 average time/residue: 0.0632 time to fit residues: 8.8304 Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 972 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.027539 restraints weight = 82286.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028538 restraints weight = 49164.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029206 restraints weight = 35304.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029651 restraints weight = 28381.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.029955 restraints weight = 24518.636| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9408 Z= 0.132 Angle : 0.481 7.177 12746 Z= 0.247 Chirality : 0.035 0.257 1472 Planarity : 0.002 0.030 1603 Dihedral : 13.780 172.050 1479 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 57.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.30 % Allowed : 28.79 % Favored : 66.91 % 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: 1.57 (0.26), residues: 1170 helix: 2.26 (0.19), residues: 777 sheet: -0.94 (0.62), residues: 82 loop : -1.64 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1091 TYR 0.006 0.001 TYR A 996 PHE 0.020 0.001 PHE A 140 TRP 0.006 0.001 TRP A 960 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9408) covalent geometry : angle 0.48091 / 0.25 (12746) hydrogen bonds : bond 0.03856 / 2.42 ( 596) hydrogen bonds : angle 3.95197 / 2.83 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 54 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9468 (p0) cc_final: 0.9252 (p0) REVERT: A 194 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.8913 (mmmm) REVERT: A 304 MET cc_start: 0.9605 (mmp) cc_final: 0.9150 (mmp) REVERT: A 306 PHE cc_start: 0.9616 (OUTLIER) cc_final: 0.9159 (t80) REVERT: A 310 MET cc_start: 0.9397 (mmm) cc_final: 0.8884 (mmm) REVERT: A 344 LEU cc_start: 0.9639 (tp) cc_final: 0.9308 (tt) REVERT: A 348 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: A 621 MET cc_start: 0.9117 (mmm) cc_final: 0.8687 (mmm) REVERT: A 784 MET cc_start: 0.9238 (tmm) cc_final: 0.8752 (tmm) REVERT: A 957 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 1007 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9408 (mm) outliers start: 42 outliers final: 35 residues processed: 91 average time/residue: 0.0675 time to fit residues: 9.6012 Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 54 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.0570 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028003 restraints weight = 81206.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029011 restraints weight = 48476.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029707 restraints weight = 34590.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030151 restraints weight = 27572.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030480 restraints weight = 23757.128| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9408 Z= 0.104 Angle : 0.460 7.678 12746 Z= 0.233 Chirality : 0.035 0.268 1472 Planarity : 0.002 0.028 1603 Dihedral : 13.468 177.434 1478 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 54.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.10 % Allowed : 29.00 % Favored : 66.91 % 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: 1.85 (0.26), residues: 1170 helix: 2.43 (0.19), residues: 778 sheet: -0.73 (0.62), residues: 81 loop : -1.44 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 598 TYR 0.004 0.001 TYR A 122 PHE 0.023 0.001 PHE A 140 TRP 0.003 0.001 TRP A 320 HIS 0.005 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 ( 9408) covalent geometry : angle 0.46006 / 0.23 (12746) hydrogen bonds : bond 0.03677 / 2.31 ( 596) hydrogen bonds : angle 3.75773 / 2.69 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9469 (p0) cc_final: 0.9260 (p0) REVERT: A 304 MET cc_start: 0.9609 (mmp) cc_final: 0.9108 (mmp) REVERT: A 306 PHE cc_start: 0.9598 (OUTLIER) cc_final: 0.9140 (t80) REVERT: A 310 MET cc_start: 0.9386 (mmm) cc_final: 0.8855 (mmm) REVERT: A 348 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: A 621 MET cc_start: 0.9107 (mmm) cc_final: 0.8689 (mmm) REVERT: A 784 MET cc_start: 0.9227 (tmm) cc_final: 0.8839 (tmm) REVERT: A 957 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8500 (t80) REVERT: A 1007 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9404 (mm) REVERT: A 1162 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8699 (mtm-85) outliers start: 40 outliers final: 31 residues processed: 90 average time/residue: 0.0742 time to fit residues: 10.5539 Evaluate side-chains 89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.028148 restraints weight = 80877.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.029137 restraints weight = 48017.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.029828 restraints weight = 34440.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030249 restraints weight = 27440.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030597 restraints weight = 23741.152| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9408 Z= 0.104 Angle : 0.463 7.667 12746 Z= 0.234 Chirality : 0.035 0.274 1472 Planarity : 0.002 0.029 1603 Dihedral : 13.100 175.769 1476 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 55.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.89 % Allowed : 29.51 % Favored : 66.60 % 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: 1.99 (0.26), residues: 1170 helix: 2.54 (0.19), residues: 777 sheet: -0.74 (0.62), residues: 82 loop : -1.36 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1091 TYR 0.006 0.001 TYR A1042 PHE 0.020 0.001 PHE A 140 TRP 0.003 0.001 TRP A 167 HIS 0.006 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 9408) covalent geometry : angle 0.46323 / 0.23 (12746) hydrogen bonds : bond 0.03624 / 2.30 ( 596) hydrogen bonds : angle 3.71152 / 2.65 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 54 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.9443 (p0) cc_final: 0.9205 (p0) REVERT: A 194 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8909 (mmmm) REVERT: A 304 MET cc_start: 0.9610 (mmp) cc_final: 0.9100 (mmp) REVERT: A 306 PHE cc_start: 0.9606 (OUTLIER) cc_final: 0.9115 (t80) REVERT: A 310 MET cc_start: 0.9391 (mmm) cc_final: 0.8823 (mmm) REVERT: A 348 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8582 (m-10) REVERT: A 550 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9136 (pp) REVERT: A 621 MET cc_start: 0.9155 (mmm) cc_final: 0.8715 (mmm) REVERT: A 784 MET cc_start: 0.9201 (tmm) cc_final: 0.8813 (tmm) REVERT: A 957 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 1007 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9398 (mm) REVERT: A 1162 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8703 (mtm-85) outliers start: 38 outliers final: 29 residues processed: 86 average time/residue: 0.0766 time to fit residues: 10.3036 Evaluate side-chains 89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 348 PHE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1038 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1084 PHE Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1225 CYS Chi-restraints excluded: chain A residue 1255 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 446 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028352 restraints weight = 80422.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029361 restraints weight = 47546.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030042 restraints weight = 33879.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.030512 restraints weight = 27091.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030816 restraints weight = 23181.045| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9408 Z= 0.100 Angle : 0.460 7.726 12746 Z= 0.231 Chirality : 0.035 0.284 1472 Planarity : 0.002 0.029 1603 Dihedral : 12.461 161.696 1476 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 54.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.69 % Allowed : 29.82 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.22 (0.26), residues: 1170 helix: 2.67 (0.19), residues: 778 sheet: -0.50 (0.62), residues: 80 loop : -1.21 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.005 0.001 TYR A1042 PHE 0.020 0.001 PHE A 140 TRP 0.003 0.001 TRP A 167 HIS 0.006 0.001 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 9408) covalent geometry : angle 0.45975 / 0.23 (12746) hydrogen bonds : bond 0.03456 / 2.19 ( 596) hydrogen bonds : angle 3.59631 / 2.57 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.18 seconds wall clock time: 25 minutes 16.92 seconds (1516.92 seconds total)