Starting phenix.real_space_refine on Fri Oct 23 19:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vt1_65312/10_2026/9vt1_65312.map" } resolution = 2.46 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= -0.001 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6837 2.51 5 N 1761 2.21 5 O 1935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10542 Classifications: {'peptide': 1319} Link IDs: {'PTRANS': 53, 'TRANS': 1265} Chain breaks: 5 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10602 At special positions: 0 Unit cell: (130.503, 92.307, 112.466, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 1 11.99 O 1935 8.00 N 1761 7.00 C 6837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1402 " - pdb=" SG CYS A1444 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1441 " distance=2.02 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: 0.94 Conformation dependent library (CDL) restraints added in 539.9 milliseconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 61.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.729A pdb=" N ARG A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 445 through 462 Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 512 through 533 removed outlier: 3.792A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 571 removed outlier: 3.577A pdb=" N VAL A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 585 through 616 Proline residue: A 599 - end of helix removed outlier: 3.828A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 649 removed outlier: 3.720A pdb=" N VAL A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 689 removed outlier: 4.238A pdb=" N TRP A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 687 " --> pdb=" O TRP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.752A pdb=" N TYR A 695 " --> pdb=" O ASN A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 removed outlier: 3.711A pdb=" N GLU A 723 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 760 through 786 removed outlier: 3.716A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 804 removed outlier: 4.181A pdb=" N LYS A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 800 through 804' Processing helix chain 'A' and resid 900 through 909 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 951 through 964 Processing helix chain 'A' and resid 969 through 984 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.702A pdb=" N ALA A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.527A pdb=" N ALA A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'A' and resid 1091 through 1101 Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1131 through 1138 Processing helix chain 'A' and resid 1139 through 1158 removed outlier: 3.511A pdb=" N GLN A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1169 removed outlier: 3.689A pdb=" N LEU A1168 " --> pdb=" O PRO A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1192 Processing helix chain 'A' and resid 1193 through 1215 removed outlier: 3.539A pdb=" N PHE A1215 " --> pdb=" O ASN A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1236 removed outlier: 3.850A pdb=" N GLN A1226 " --> pdb=" O MET A1222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A1236 " --> pdb=" O VAL A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1260 Proline residue: A1248 - end of helix removed outlier: 3.554A pdb=" N GLN A1253 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1265 Processing helix chain 'A' and resid 1268 through 1297 removed outlier: 3.865A pdb=" N GLU A1280 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Proline residue: A1282 - end of helix removed outlier: 4.171A pdb=" N TYR A1297 " --> pdb=" O PHE A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1314 through 1339 removed outlier: 4.181A pdb=" N PHE A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1360 Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1374 through 1381 Processing helix chain 'A' and resid 1381 through 1396 removed outlier: 3.972A pdb=" N TYR A1385 " --> pdb=" O ASN A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1417 through 1430 Proline residue: A1424 - end of helix removed outlier: 3.978A pdb=" N PHE A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1456 removed outlier: 4.221A pdb=" N PHE A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1489 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 177 removed outlier: 6.239A pdb=" N ILE A 169 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLY A 132 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS A 171 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA A 130 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA A 175 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 126 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET A 177 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLY A 124 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 177 removed outlier: 6.239A pdb=" N ILE A 169 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLY A 132 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS A 171 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA A 130 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA A 175 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 126 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET A 177 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLY A 124 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.815A pdb=" N VAL A 374 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 385 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.852A pdb=" N GLU A 422 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AA7, first strand: chain 'A' and resid 874 through 885 removed outlier: 6.351A pdb=" N TYR A 866 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 879 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 864 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 881 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 862 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY A 883 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE A 860 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 864 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 919 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR A 866 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 917 " --> pdb=" O TYR A 866 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 937 through 940 removed outlier: 6.170A pdb=" N GLY A 938 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP A1026 " --> pdb=" O GLY A 938 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 940 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A1023 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR A1057 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A1025 " --> pdb=" O THR A1057 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 890 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU A1073 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 892 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU A1075 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET A 894 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A1083 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A1076 " --> pdb=" O THR A1081 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR A1081 " --> pdb=" O GLN A1076 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1408 through 1410 591 hydrogen bonds defined for protein. 1719 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: 1.98 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2580 1.33 - 1.45: 2396 1.45 - 1.57: 5796 1.57 - 1.69: 4 1.69 - 1.81: 103 Bond restraints: 10879 Sorted by residual: bond pdb=" C5 ATP A1703 " pdb=" N7 ATP A1703 " ideal model delta sigma weight residual 1.387 1.307 0.080 1.00e-02 1.00e+04 6.36e+01 bond pdb=" C4 ADP A1702 " pdb=" C5 ADP A1702 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O3A ATP A1703 " pdb=" PB ATP A1703 " ideal model delta sigma weight residual 1.592 1.541 0.051 1.10e-02 8.26e+03 2.15e+01 bond pdb=" C5 ADP A1702 " pdb=" C6 ADP A1702 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O5' ATP A1703 " pdb=" PA ATP A1703 " ideal model delta sigma weight residual 1.579 1.610 -0.031 1.10e-02 8.26e+03 7.94e+00 ... (remaining 10874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 14687 4.00 - 7.99: 56 7.99 - 11.99: 9 11.99 - 15.98: 2 15.98 - 19.98: 2 Bond angle restraints: 14756 Sorted by residual: angle pdb=" PB ATP A1703 " pdb=" O3B ATP A1703 " pdb=" PG ATP A1703 " ideal model delta sigma weight residual 139.87 119.89 19.98 1.00e+00 1.00e+00 3.99e+02 angle pdb=" PA ATP A1703 " pdb=" O3A ATP A1703 " pdb=" PB ATP A1703 " ideal model delta sigma weight residual 136.83 119.06 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" O3B ATP A1703 " pdb=" PG ATP A1703 " pdb=" O3G ATP A1703 " ideal model delta sigma weight residual 104.48 117.56 -13.08 1.14e+00 7.76e-01 1.33e+02 angle pdb=" C GLN A1223 " pdb=" N GLY A1224 " pdb=" CA GLY A1224 " ideal model delta sigma weight residual 119.98 126.78 -6.80 1.11e+00 8.12e-01 3.76e+01 angle pdb=" O2G ATP A1703 " pdb=" PG ATP A1703 " pdb=" O3B ATP A1703 " ideal model delta sigma weight residual 104.48 110.95 -6.47 1.14e+00 7.76e-01 3.25e+01 ... (remaining 14751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.56: 6092 33.56 - 67.11: 283 67.11 - 100.67: 18 100.67 - 134.22: 1 134.22 - 167.78: 1 Dihedral angle restraints: 6395 sinusoidal: 2553 harmonic: 3842 Sorted by residual: dihedral pdb=" CB CYS A1402 " pdb=" SG CYS A1402 " pdb=" SG CYS A1444 " pdb=" CB CYS A1444 " ideal model delta sinusoidal sigma weight residual -86.00 -172.77 86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" O2A ADP A1702 " pdb=" O3A ADP A1702 " pdb=" PA ADP A1702 " pdb=" PB ADP A1702 " ideal model delta sinusoidal sigma weight residual -60.00 107.78 -167.78 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A1702 " pdb=" O3A ADP A1702 " pdb=" PB ADP A1702 " pdb=" PA ADP A1702 " ideal model delta sinusoidal sigma weight residual -60.00 64.55 -124.56 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1387 0.069 - 0.138: 187 0.138 - 0.207: 13 0.207 - 0.276: 4 0.276 - 0.345: 2 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA TYR A 125 " pdb=" N TYR A 125 " pdb=" C TYR A 125 " pdb=" CB TYR A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA PRO A1238 " pdb=" N PRO A1238 " pdb=" C PRO A1238 " pdb=" CB PRO A1238 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA PRO A 739 " pdb=" N PRO A 739 " pdb=" C PRO A 739 " pdb=" CB PRO A 739 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1590 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1233 " 0.044 2.00e-02 2.50e+03 2.99e-02 1.56e+01 pdb=" CG PHE A1233 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A1233 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A1233 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE A1233 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A1233 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A1233 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 673 " -0.045 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A 673 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 673 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 673 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 673 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 673 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 673 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1452 " -0.041 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE A1452 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A1452 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A1452 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A1452 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1452 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A1452 " -0.026 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 77 2.57 - 3.15: 8452 3.15 - 3.74: 17811 3.74 - 4.32: 25064 4.32 - 4.90: 40901 Nonbonded interactions: 92305 Sorted by model distance: nonbonded pdb=" OG1 THR A 902 " pdb="MG MG A1701 " model vdw 1.990 2.170 nonbonded pdb=" OD1 ASP A 163 " pdb=" N SER A 164 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR A 613 " pdb=" O ARG A 619 " model vdw 2.208 3.040 nonbonded pdb=" O LEU A 905 " pdb=" OG SER A 909 " model vdw 2.235 3.040 nonbonded pdb=" O CYS A1357 " pdb=" ND2 ASN A1381 " model vdw 2.251 3.120 ... (remaining 92300 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 10882 Z= 0.280 Angle : 0.793 19.980 14762 Z= 0.506 Chirality : 0.048 0.345 1593 Planarity : 0.005 0.058 1867 Dihedral : 17.537 167.781 3928 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.01 % Rotamer: Outliers : 3.65 % Allowed : 19.95 % Favored : 76.40 % 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: 1.34 (0.23), residues: 1307 helix: 1.53 (0.19), residues: 737 sheet: -0.63 (0.47), residues: 94 loop : 0.35 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 685 TYR 0.035 0.002 TYR A 361 PHE 0.045 0.003 PHE A1215 TRP 0.029 0.002 TRP A 326 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.28 (10879) covalent geometry : angle 0.79235 / 0.51 (14756) SS BOND : bond 0.00545 / 0.27 ( 3) SS BOND : angle 2.01196 / 1.33 ( 6) hydrogen bonds : bond 0.12742 / 8.58 ( 589) hydrogen bonds : angle 5.89746 / 4.15 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 35 residues processed: 199 average time/residue: 0.5135 time to fit residues: 110.7920 Evaluate side-chains 189 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 941 GLN A1076 GLN A1245 GLN ** A1334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106608 restraints weight = 11838.228| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.77 r_work: 0.3077 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10882 Z= 0.113 Angle : 0.490 6.596 14762 Z= 0.255 Chirality : 0.039 0.133 1593 Planarity : 0.004 0.037 1867 Dihedral : 10.244 175.266 1553 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.01 % Rotamer: Outliers : 3.29 % Allowed : 18.34 % Favored : 78.36 % 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: 1.80 (0.23), residues: 1307 helix: 2.00 (0.19), residues: 741 sheet: -0.73 (0.47), residues: 94 loop : 0.43 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 685 TYR 0.012 0.001 TYR A1249 PHE 0.015 0.001 PHE A1233 TRP 0.012 0.001 TRP A 634 HIS 0.002 0.000 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10879) covalent geometry : angle 0.48960 / 0.26 (14756) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 0.60362 / 0.38 ( 6) hydrogen bonds : bond 0.04085 / 2.63 ( 589) hydrogen bonds : angle 4.27795 / 3.01 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: A 461 GLU cc_start: 0.6964 (tp30) cc_final: 0.6653 (tt0) REVERT: A 685 ARG cc_start: 0.7482 (mmt-90) cc_final: 0.6948 (mpp80) REVERT: A 725 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 910 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7261 (mm-30) REVERT: A 1004 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 1356 MET cc_start: 0.8093 (mmm) cc_final: 0.7656 (mmm) outliers start: 37 outliers final: 17 residues processed: 192 average time/residue: 0.5450 time to fit residues: 112.8735 Evaluate side-chains 177 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [106, 52, 62, 10, 130, 34, 70, 92, 56, 67, 4] chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 0.0170 chunk 4 optimal weight: 0.0270 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109738 restraints weight = 11889.317| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.75 r_work: 0.3120 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10882 Z= 0.096 Angle : 0.455 5.999 14762 Z= 0.235 Chirality : 0.038 0.129 1593 Planarity : 0.003 0.037 1867 Dihedral : 8.952 175.597 1511 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 19.15 % Favored : 78.18 % 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: 2.01 (0.23), residues: 1307 helix: 2.22 (0.18), residues: 734 sheet: -0.43 (0.51), residues: 84 loop : 0.38 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1379 TYR 0.010 0.001 TYR A1249 PHE 0.016 0.001 PHE A 494 TRP 0.011 0.001 TRP A 634 HIS 0.002 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 (10879) covalent geometry : angle 0.45520 / 0.23 (14756) SS BOND : bond 0.00638 / 0.32 ( 3) SS BOND : angle 0.69630 / 0.46 ( 6) hydrogen bonds : bond 0.03534 / 2.27 ( 589) hydrogen bonds : angle 4.01295 / 2.81 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.7218 (t0) cc_final: 0.7017 (t0) REVERT: A 340 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: A 461 GLU cc_start: 0.7025 (tp30) cc_final: 0.6703 (tt0) REVERT: A 910 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7304 (mm-30) REVERT: A 921 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: A 1004 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: A 1219 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6192 (ptmt) REVERT: A 1334 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 1356 MET cc_start: 0.7967 (mmm) cc_final: 0.7568 (mmm) REVERT: A 1373 PHE cc_start: 0.7178 (t80) cc_final: 0.6957 (t80) REVERT: A 1454 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7714 (tmtt) outliers start: 30 outliers final: 13 residues processed: 194 average time/residue: 0.5204 time to fit residues: 109.4286 Evaluate side-chains 183 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 921 GLU Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1334 GLN Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [94, 56, 6, 61, 23, 45, 82, 37, 128, 127, 40] chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A1334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101287 restraints weight = 11995.581| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.71 r_work: 0.3033 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10882 Z= 0.246 Angle : 0.592 7.982 14762 Z= 0.308 Chirality : 0.045 0.177 1593 Planarity : 0.004 0.042 1867 Dihedral : 9.420 173.069 1507 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % Rotamer: Outliers : 3.12 % Allowed : 18.52 % Favored : 78.36 % 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: 1.54 (0.22), residues: 1307 helix: 1.82 (0.18), residues: 733 sheet: -0.76 (0.46), residues: 88 loop : 0.26 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 685 TYR 0.021 0.002 TYR A1249 PHE 0.021 0.002 PHE A 625 TRP 0.017 0.002 TRP A 634 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (10879) covalent geometry : angle 0.59134 / 0.31 (14756) SS BOND : bond 0.00359 / 0.17 ( 3) SS BOND : angle 1.66032 / 1.09 ( 6) hydrogen bonds : bond 0.05000 / 3.23 ( 589) hydrogen bonds : angle 4.31376 / 3.02 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8876 (ptp) cc_final: 0.8260 (ptp) REVERT: A 461 GLU cc_start: 0.7067 (tp30) cc_final: 0.6756 (tt0) REVERT: A 639 MET cc_start: 0.8550 (mmm) cc_final: 0.8293 (mmp) REVERT: A 725 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7588 (tp) REVERT: A 910 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7438 (mm-30) REVERT: A 1356 MET cc_start: 0.8160 (mmm) cc_final: 0.7777 (mmm) outliers start: 35 outliers final: 19 residues processed: 186 average time/residue: 0.5277 time to fit residues: 106.4198 Evaluate side-chains 182 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1155 GLU Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [9, 39, 83, 24, 109, 42, 95, 4, 113, 43, 98] chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 382 GLN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105554 restraints weight = 11848.233| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.70 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10882 Z= 0.112 Angle : 0.484 6.238 14762 Z= 0.251 Chirality : 0.039 0.133 1593 Planarity : 0.004 0.037 1867 Dihedral : 8.331 159.384 1500 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 20.57 % Favored : 77.38 % 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: 1.74 (0.23), residues: 1307 helix: 2.01 (0.18), residues: 737 sheet: -0.82 (0.47), residues: 88 loop : 0.32 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 685 TYR 0.012 0.001 TYR A1249 PHE 0.012 0.001 PHE A1233 TRP 0.016 0.001 TRP A 634 HIS 0.002 0.000 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10879) covalent geometry : angle 0.48390 / 0.25 (14756) SS BOND : bond 0.00317 / 0.16 ( 3) SS BOND : angle 1.25841 / 0.82 ( 6) hydrogen bonds : bond 0.03848 / 2.46 ( 589) hydrogen bonds : angle 4.07476 / 2.85 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8700 (ptp) cc_final: 0.8134 (ptp) REVERT: A 461 GLU cc_start: 0.7033 (tp30) cc_final: 0.6712 (tt0) REVERT: A 704 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: A 910 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7358 (mm-30) REVERT: A 911 ARG cc_start: 0.6986 (mtp180) cc_final: 0.6771 (mtp85) REVERT: A 1004 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: A 1219 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6214 (ptmt) REVERT: A 1356 MET cc_start: 0.8059 (mmm) cc_final: 0.7704 (mmm) REVERT: A 1462 GLU cc_start: 0.8155 (pt0) cc_final: 0.7943 (pt0) outliers start: 23 outliers final: 12 residues processed: 184 average time/residue: 0.5644 time to fit residues: 112.0431 Evaluate side-chains 176 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [93, 116, 127, 55, 7, 12, 98, 57, 4, 71, 105] chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 382 GLN A 522 GLN A1334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104210 restraints weight = 11955.258| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.71 r_work: 0.3076 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10882 Z= 0.143 Angle : 0.504 6.312 14762 Z= 0.262 Chirality : 0.040 0.134 1593 Planarity : 0.004 0.038 1867 Dihedral : 8.075 147.725 1500 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.84 % Favored : 98.09 % Rotamer: Outliers : 2.94 % Allowed : 20.04 % Favored : 77.03 % 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: 1.72 (0.23), residues: 1307 helix: 1.98 (0.18), residues: 737 sheet: -0.85 (0.46), residues: 88 loop : 0.32 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 685 TYR 0.015 0.002 TYR A1249 PHE 0.015 0.001 PHE A1233 TRP 0.014 0.001 TRP A 634 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10879) covalent geometry : angle 0.50372 / 0.26 (14756) SS BOND : bond 0.00270 / 0.13 ( 3) SS BOND : angle 1.17258 / 0.77 ( 6) hydrogen bonds : bond 0.04112 / 2.64 ( 589) hydrogen bonds : angle 4.08072 / 2.86 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8739 (ptp) cc_final: 0.8166 (ptp) REVERT: A 461 GLU cc_start: 0.7029 (tp30) cc_final: 0.6706 (tt0) REVERT: A 704 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: A 910 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7407 (mm-30) REVERT: A 1219 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6215 (ptmt) REVERT: A 1356 MET cc_start: 0.8091 (mmm) cc_final: 0.7734 (mmm) REVERT: A 1462 GLU cc_start: 0.8157 (pt0) cc_final: 0.7933 (pt0) outliers start: 33 outliers final: 20 residues processed: 186 average time/residue: 0.5337 time to fit residues: 107.5380 Evaluate side-chains 183 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1152 MET Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [9, 114, 11, 130, 62, 86, 34, 19, 21, 128, 101] chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 128 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 382 GLN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106115 restraints weight = 11899.945| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.68 r_work: 0.3074 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10882 Z= 0.113 Angle : 0.479 6.319 14762 Z= 0.248 Chirality : 0.039 0.131 1593 Planarity : 0.004 0.038 1867 Dihedral : 7.383 127.288 1500 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.61 % Favored : 98.32 % Rotamer: Outliers : 2.58 % Allowed : 20.39 % Favored : 77.03 % 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 (0.23), residues: 1307 helix: 2.09 (0.18), residues: 737 sheet: -0.70 (0.46), residues: 93 loop : 0.37 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 911 TYR 0.012 0.001 TYR A1249 PHE 0.012 0.001 PHE A1233 TRP 0.014 0.001 TRP A 634 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10879) covalent geometry : angle 0.47833 / 0.25 (14756) SS BOND : bond 0.00225 / 0.11 ( 3) SS BOND : angle 1.00396 / 0.66 ( 6) hydrogen bonds : bond 0.03751 / 2.40 ( 589) hydrogen bonds : angle 3.99215 / 2.79 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8678 (ptp) cc_final: 0.8265 (ptp) REVERT: A 461 GLU cc_start: 0.6991 (tp30) cc_final: 0.6671 (tt0) REVERT: A 704 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 786 ASN cc_start: 0.7484 (t0) cc_final: 0.7244 (t0) REVERT: A 910 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7399 (mm-30) REVERT: A 1219 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6206 (ptmt) REVERT: A 1356 MET cc_start: 0.8046 (mmm) cc_final: 0.7668 (mmm) outliers start: 29 outliers final: 19 residues processed: 185 average time/residue: 0.5450 time to fit residues: 109.1889 Evaluate side-chains 180 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1152 MET Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [93, 121, 90, 30, 64, 31, 68, 8, 15, 126, 47] chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.105334 restraints weight = 11879.821| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.76 r_work: 0.3059 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10882 Z= 0.131 Angle : 0.496 6.405 14762 Z= 0.256 Chirality : 0.040 0.133 1593 Planarity : 0.004 0.042 1867 Dihedral : 7.253 112.927 1500 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 2.85 % Allowed : 20.48 % Favored : 76.67 % 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: 1.80 (0.23), residues: 1307 helix: 2.04 (0.18), residues: 739 sheet: -0.71 (0.46), residues: 93 loop : 0.35 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 911 TYR 0.014 0.001 TYR A1249 PHE 0.014 0.001 PHE A1233 TRP 0.013 0.001 TRP A 634 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10879) covalent geometry : angle 0.49583 / 0.26 (14756) SS BOND : bond 0.00242 / 0.12 ( 3) SS BOND : angle 1.07232 / 0.70 ( 6) hydrogen bonds : bond 0.03922 / 2.51 ( 589) hydrogen bonds : angle 4.01451 / 2.81 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 173 MET cc_start: 0.8697 (ptp) cc_final: 0.8281 (ptp) REVERT: A 461 GLU cc_start: 0.6992 (tp30) cc_final: 0.6680 (tt0) REVERT: A 671 THR cc_start: 0.8437 (t) cc_final: 0.8216 (m) REVERT: A 786 ASN cc_start: 0.7432 (t0) cc_final: 0.7183 (t0) REVERT: A 910 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7359 (mm-30) REVERT: A 939 TYR cc_start: 0.6148 (p90) cc_final: 0.5675 (p90) REVERT: A 1004 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: A 1219 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6194 (ptmt) REVERT: A 1334 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: A 1356 MET cc_start: 0.8031 (mmm) cc_final: 0.7638 (mmm) outliers start: 32 outliers final: 22 residues processed: 186 average time/residue: 0.5264 time to fit residues: 106.2154 Evaluate side-chains 186 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1152 MET Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1334 GLN Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [72, 16, 70, 58, 0, 59, 99, 41, 98, 121, 22] chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102328 restraints weight = 11915.240| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.76 r_work: 0.3041 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10882 Z= 0.207 Angle : 0.567 6.921 14762 Z= 0.295 Chirality : 0.043 0.161 1593 Planarity : 0.004 0.039 1867 Dihedral : 7.707 100.319 1500 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.58 % Allowed : 20.84 % Favored : 76.58 % 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: 1.52 (0.23), residues: 1307 helix: 1.81 (0.18), residues: 737 sheet: -0.83 (0.45), residues: 88 loop : 0.22 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 685 TYR 0.020 0.002 TYR A1249 PHE 0.019 0.002 PHE A 625 TRP 0.015 0.002 TRP A 634 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (10879) covalent geometry : angle 0.56685 / 0.29 (14756) SS BOND : bond 0.00297 / 0.14 ( 3) SS BOND : angle 1.33698 / 0.87 ( 6) hydrogen bonds : bond 0.04653 / 2.98 ( 589) hydrogen bonds : angle 4.21549 / 2.96 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8772 (ptp) cc_final: 0.8384 (ptp) REVERT: A 401 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8056 (ttpp) REVERT: A 461 GLU cc_start: 0.7138 (tp30) cc_final: 0.6808 (tt0) REVERT: A 786 ASN cc_start: 0.7547 (t0) cc_final: 0.7339 (t0) REVERT: A 910 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7442 (mm-30) REVERT: A 1356 MET cc_start: 0.8148 (mmm) cc_final: 0.7740 (mmm) REVERT: A 1462 GLU cc_start: 0.8146 (pt0) cc_final: 0.7923 (pt0) outliers start: 29 outliers final: 22 residues processed: 185 average time/residue: 0.5124 time to fit residues: 102.7635 Evaluate side-chains 185 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1152 MET Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [28, 36, 59, 53, 44, 124, 75, 74, 2, 87, 120] chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 522 GLN ** A1334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104050 restraints weight = 11877.992| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.75 r_work: 0.3041 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10882 Z= 0.145 Angle : 0.519 6.395 14762 Z= 0.270 Chirality : 0.041 0.136 1593 Planarity : 0.004 0.053 1867 Dihedral : 7.351 91.747 1500 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.84 % Favored : 98.09 % Rotamer: Outliers : 2.23 % Allowed : 21.28 % Favored : 76.49 % 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: 1.64 (0.23), residues: 1307 helix: 1.94 (0.18), residues: 735 sheet: -0.79 (0.46), residues: 88 loop : 0.24 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 911 TYR 0.016 0.002 TYR A 939 PHE 0.014 0.001 PHE A1233 TRP 0.018 0.001 TRP A 634 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10879) covalent geometry : angle 0.51899 / 0.27 (14756) SS BOND : bond 0.00291 / 0.14 ( 3) SS BOND : angle 1.19054 / 0.78 ( 6) hydrogen bonds : bond 0.04145 / 2.65 ( 589) hydrogen bonds : angle 4.12183 / 2.89 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.8720 (ptp) cc_final: 0.8329 (ptp) REVERT: A 461 GLU cc_start: 0.7122 (tp30) cc_final: 0.6803 (tt0) REVERT: A 786 ASN cc_start: 0.7538 (t0) cc_final: 0.7330 (t0) REVERT: A 939 TYR cc_start: 0.6445 (p90) cc_final: 0.5951 (p90) REVERT: A 1356 MET cc_start: 0.8116 (mmm) cc_final: 0.7699 (mmm) REVERT: A 1462 GLU cc_start: 0.8134 (pt0) cc_final: 0.7909 (pt0) outliers start: 25 outliers final: 22 residues processed: 182 average time/residue: 0.5175 time to fit residues: 102.1013 Evaluate side-chains 185 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1152 MET Chi-restraints excluded: chain A residue 1177 LYS Chi-restraints excluded: chain A residue 1287 VAL Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [108, 76, 79, 129, 94, 102, 93, 52, 13, 40, 44] chunk 108 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 382 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.105912 restraints weight = 11945.093| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.75 r_work: 0.3068 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10882 Z= 0.117 Angle : 0.494 6.202 14762 Z= 0.255 Chirality : 0.039 0.132 1593 Planarity : 0.004 0.043 1867 Dihedral : 6.833 76.015 1500 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 21.73 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.23), residues: 1307 helix: 2.06 (0.19), residues: 735 sheet: -0.62 (0.45), residues: 93 loop : 0.29 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 911 TYR 0.013 0.001 TYR A1249 PHE 0.012 0.001 PHE A1233 TRP 0.018 0.001 TRP A 634 HIS 0.002 0.000 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10879) covalent geometry : angle 0.49343 / 0.25 (14756) SS BOND : bond 0.00280 / 0.14 ( 3) SS BOND : angle 0.99551 / 0.65 ( 6) hydrogen bonds : bond 0.03793 / 2.42 ( 589) hydrogen bonds : angle 4.02476 / 2.82 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3901.00 seconds wall clock time: 67 minutes 9.81 seconds (4029.81 seconds total)