Starting phenix.real_space_refine on Fri Jul 3 06:43:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.cif Found real_map, /net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.map" model { file = "/net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9edb_47943/07_2026/9edb_47943.cif" } resolution = 3.1 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 122 5.49 5 S 20 5.16 5 C 7595 2.51 5 N 2239 2.21 5 O 2660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12636 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10049 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1342, 10049 Classifications: {'peptide': 1342} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 35, 'TRANS': 1306} Chain breaks: 4 Unresolved non-hydrogen bonds: 948 Unresolved non-hydrogen angles: 1163 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 49, 'ASN:plan1': 16, 'ARG:plan': 18, 'GLN:plan1': 12, 'TYR:plan': 5, 'PHE:plan': 4, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 529 Chain: "B" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1909 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 77} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.87, per 1000 atoms: 0.23 Number of scatterers: 12636 At special positions: 0 Unit cell: (99.1508, 127.48, 124.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 122 15.00 O 2660 8.00 N 2239 7.00 C 7595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 537.4 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 11 sheets defined 53.9% alpha, 7.2% beta 39 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.247A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.950A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.773A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.518A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.990A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.322A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.861A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.659A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.754A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.730A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.795A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.529A pdb=" N VAL A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.602A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.709A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 792 Processing helix chain 'A' and resid 802 through 806 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.737A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.073A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.592A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.997A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.505A pdb=" N ILE A1022 " --> pdb=" O VAL A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1075 through 1088 removed outlier: 3.669A pdb=" N ALA A1081 " --> pdb=" O GLY A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.089A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.842A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.643A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.784A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 removed outlier: 3.720A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.672A pdb=" N ILE A 759 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 956 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.082A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.793A pdb=" N THR A 466 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.863A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 560 removed outlier: 4.050A pdb=" N VAL A 559 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA8, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB1, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.539A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1324 through 1325 498 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 1.30 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: 3108 1.33 - 1.46: 3394 1.46 - 1.58: 6345 1.58 - 1.70: 242 1.70 - 1.82: 38 Bond restraints: 13127 Sorted by residual: bond pdb=" C3' DC C -2 " pdb=" O3' DC C -2 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" C3' DT D 44 " pdb=" C2' DT D 44 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DC D 38 " pdb=" C2' DC D 38 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.41e+00 bond pdb=" C1' DT C 0 " pdb=" N1 DT C 0 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.88e+00 bond pdb=" C3' DT C 0 " pdb=" C2' DT C 0 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.63e+00 ... (remaining 13122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 18095 3.15 - 6.30: 209 6.30 - 9.45: 38 9.45 - 12.59: 8 12.59 - 15.74: 1 Bond angle restraints: 18351 Sorted by residual: angle pdb=" C1' C B 60 " pdb=" N1 C B 60 " pdb=" C2 C B 60 " ideal model delta sigma weight residual 118.80 125.80 -7.00 1.10e+00 8.26e-01 4.05e+01 angle pdb=" C1' C B 18 " pdb=" N1 C B 18 " pdb=" C2 C B 18 " ideal model delta sigma weight residual 118.80 125.72 -6.92 1.10e+00 8.26e-01 3.96e+01 angle pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sigma weight residual 118.80 125.63 -6.83 1.10e+00 8.26e-01 3.85e+01 angle pdb=" CA LYS A1085 " pdb=" CB LYS A1085 " pdb=" CG LYS A1085 " ideal model delta sigma weight residual 114.10 126.45 -12.35 2.00e+00 2.50e-01 3.81e+01 angle pdb=" CA LYS A 710 " pdb=" CB LYS A 710 " pdb=" CG LYS A 710 " ideal model delta sigma weight residual 114.10 126.04 -11.94 2.00e+00 2.50e-01 3.56e+01 ... (remaining 18346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7367 34.47 - 68.95: 483 68.95 - 103.42: 26 103.42 - 137.90: 0 137.90 - 172.37: 4 Dihedral angle restraints: 7880 sinusoidal: 3941 harmonic: 3939 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 37.21 162.79 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U B 56 " pdb=" C1' U B 56 " pdb=" N1 U B 56 " pdb=" C2 U B 56 " ideal model delta sinusoidal sigma weight residual -128.00 -66.96 -61.04 1 1.70e+01 3.46e-03 1.71e+01 dihedral pdb=" CA PHE A 972 " pdb=" C PHE A 972 " pdb=" N TYR A 973 " pdb=" CA TYR A 973 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1827 0.063 - 0.127: 297 0.127 - 0.190: 34 0.190 - 0.254: 6 0.254 - 0.317: 3 Chirality restraints: 2167 Sorted by residual: chirality pdb=" CG LEU A 423 " pdb=" CB LEU A 423 " pdb=" CD1 LEU A 423 " pdb=" CD2 LEU A 423 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU A 433 " pdb=" CB LEU A 433 " pdb=" CD1 LEU A 433 " pdb=" CD2 LEU A 433 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2164 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 435 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" CG ASP A 435 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP A 435 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP A 435 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 271 " 0.017 2.00e-02 2.50e+03 2.36e-02 1.12e+01 pdb=" CG TYR A 271 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 271 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 271 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 271 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 271 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 271 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 271 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 973 " 0.023 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR A 973 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 973 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 973 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 973 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 973 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 973 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 973 " -0.001 2.00e-02 2.50e+03 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2618 2.78 - 3.31: 11220 3.31 - 3.84: 22344 3.84 - 4.37: 25227 4.37 - 4.90: 40420 Nonbonded interactions: 101829 Sorted by model distance: nonbonded pdb=" O SER A1136 " pdb=" OG SER A1136 " model vdw 2.248 3.040 nonbonded pdb=" O LYS A 209 " pdb=" OG SER A 213 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 909 " pdb=" OD2 ASP A 912 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.311 3.040 nonbonded pdb=" O ILE A 305 " pdb=" OG SER A 320 " model vdw 2.313 3.040 ... (remaining 101824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.880 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.650 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 0.064 13127 Z= 0.306 Angle : 0.913 15.744 18351 Z= 0.578 Chirality : 0.049 0.317 2167 Planarity : 0.006 0.068 1912 Dihedral : 19.800 172.371 5328 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.53 % Allowed : 21.82 % Favored : 77.65 % 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: -2.05 (0.21), residues: 1332 helix: -0.86 (0.19), residues: 671 sheet: -0.84 (0.50), residues: 110 loop : -2.00 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 457 TYR 0.056 0.003 TYR A 271 PHE 0.042 0.003 PHE A 643 TRP 0.014 0.002 TRP A 659 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.31 (13127) covalent geometry : angle 0.91308 / 0.58 (18351) hydrogen bonds : bond 0.14612 / 9.79 ( 595) hydrogen bonds : angle 6.44790 / 4.68 ( 1633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8794 (ttp-170) cc_final: 0.8277 (ttp-170) REVERT: A 223 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7314 (pt0) REVERT: A 235 ASN cc_start: 0.8441 (m-40) cc_final: 0.7651 (t0) REVERT: A 258 LEU cc_start: 0.7965 (mm) cc_final: 0.7757 (mt) REVERT: A 395 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7202 (ttp80) REVERT: A 662 LEU cc_start: 0.7946 (mm) cc_final: 0.7707 (mm) REVERT: A 895 ARG cc_start: 0.6475 (mtp180) cc_final: 0.6183 (tpt170) REVERT: A 919 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7562 (ttt180) REVERT: A 935 LEU cc_start: 0.9136 (mt) cc_final: 0.8857 (mp) REVERT: A 1108 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8696 (mt-10) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.1105 time to fit residues: 21.3636 Evaluate side-chains 114 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 404 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 55 optimal weight: 8.9990 overall best weight: 0.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 ASN A1308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083296 restraints weight = 25976.546| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.57 r_work: 0.3105 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13127 Z= 0.149 Angle : 0.575 11.822 18351 Z= 0.318 Chirality : 0.040 0.251 2167 Planarity : 0.004 0.052 1912 Dihedral : 20.548 178.638 3152 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 18.18 % Favored : 78.82 % 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: -1.09 (0.22), residues: 1332 helix: 0.15 (0.20), residues: 676 sheet: -0.91 (0.46), residues: 123 loop : -1.76 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1078 TYR 0.023 0.001 TYR A 639 PHE 0.015 0.001 PHE A 432 TRP 0.017 0.002 TRP A1074 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (13127) covalent geometry : angle 0.57494 / 0.32 (18351) hydrogen bonds : bond 0.04830 / 3.27 ( 595) hydrogen bonds : angle 4.90425 / 3.53 ( 1633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8737 (ttp-170) cc_final: 0.8530 (ttp-170) REVERT: A 235 ASN cc_start: 0.8517 (m-40) cc_final: 0.7731 (t0) REVERT: A 258 LEU cc_start: 0.7981 (mm) cc_final: 0.7761 (mt) REVERT: A 394 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7766 (m110) REVERT: A 662 LEU cc_start: 0.8067 (mm) cc_final: 0.7847 (mm) REVERT: A 895 ARG cc_start: 0.6471 (mtp180) cc_final: 0.6102 (tpt170) REVERT: A 919 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7605 (ttm170) REVERT: A 1043 MET cc_start: 0.8646 (mmm) cc_final: 0.8416 (mmt) REVERT: A 1108 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8681 (mt-10) REVERT: A 1194 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8735 (mp) outliers start: 28 outliers final: 12 residues processed: 135 average time/residue: 0.1087 time to fit residues: 21.5744 Evaluate side-chains 117 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 chunk 55 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 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 = 0.3745 r_free = 0.3745 target = 0.114602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077179 restraints weight = 26146.287| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.60 r_work: 0.2977 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 13127 Z= 0.235 Angle : 0.625 12.240 18351 Z= 0.338 Chirality : 0.043 0.260 2167 Planarity : 0.004 0.061 1912 Dihedral : 20.612 179.672 3152 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.53 % Allowed : 18.40 % Favored : 78.07 % 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: -0.67 (0.22), residues: 1332 helix: 0.55 (0.20), residues: 674 sheet: -1.04 (0.45), residues: 125 loop : -1.55 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 654 TYR 0.017 0.002 TYR A 155 PHE 0.023 0.002 PHE A1235 TRP 0.014 0.002 TRP A 476 HIS 0.007 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (13127) covalent geometry : angle 0.62470 / 0.34 (18351) hydrogen bonds : bond 0.04866 / 3.28 ( 595) hydrogen bonds : angle 4.51022 / 3.25 ( 1633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8601 (ttp-170) REVERT: A 235 ASN cc_start: 0.8528 (m-40) cc_final: 0.7739 (t0) REVERT: A 258 LEU cc_start: 0.8008 (mm) cc_final: 0.7784 (mt) REVERT: A 895 ARG cc_start: 0.6550 (mtp180) cc_final: 0.6138 (tpt170) REVERT: A 919 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7635 (ttm170) REVERT: A 947 ASP cc_start: 0.8478 (m-30) cc_final: 0.7749 (p0) REVERT: A 1108 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8812 (mt-10) REVERT: A 1194 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8713 (mp) outliers start: 33 outliers final: 21 residues processed: 133 average time/residue: 0.0936 time to fit residues: 18.7857 Evaluate side-chains 119 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 705 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 75 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 128 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 281 GLN A 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079228 restraints weight = 25922.408| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.56 r_work: 0.3028 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13127 Z= 0.115 Angle : 0.502 11.535 18351 Z= 0.279 Chirality : 0.038 0.254 2167 Planarity : 0.003 0.049 1912 Dihedral : 20.577 179.472 3150 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.23), residues: 1332 helix: 0.85 (0.20), residues: 674 sheet: -1.03 (0.46), residues: 125 loop : -1.41 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 215 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A 432 TRP 0.011 0.001 TRP A1074 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (13127) covalent geometry : angle 0.50221 / 0.28 (18351) hydrogen bonds : bond 0.03971 / 2.69 ( 595) hydrogen bonds : angle 4.32949 / 3.14 ( 1633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8856 (ttp-170) cc_final: 0.8604 (ttp-170) REVERT: A 235 ASN cc_start: 0.8471 (m-40) cc_final: 0.7696 (t0) REVERT: A 605 ASP cc_start: 0.8777 (t0) cc_final: 0.8195 (p0) REVERT: A 746 GLU cc_start: 0.8595 (tt0) cc_final: 0.8299 (tt0) REVERT: A 895 ARG cc_start: 0.6577 (mtp180) cc_final: 0.6192 (tpt170) REVERT: A 919 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7603 (ttm170) REVERT: A 1108 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 1194 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8660 (mp) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.1031 time to fit residues: 19.0700 Evaluate side-chains 112 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1261 GLN Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 511 HIS ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 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 = 0.3734 r_free = 0.3734 target = 0.113777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076299 restraints weight = 26178.245| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.58 r_work: 0.2960 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13127 Z= 0.211 Angle : 0.555 11.177 18351 Z= 0.306 Chirality : 0.041 0.245 2167 Planarity : 0.004 0.049 1912 Dihedral : 20.536 179.681 3150 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.85 % Allowed : 18.61 % Favored : 77.54 % 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: -0.20 (0.23), residues: 1332 helix: 0.99 (0.21), residues: 674 sheet: -0.99 (0.45), residues: 131 loop : -1.36 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 215 TYR 0.017 0.002 TYR A1131 PHE 0.018 0.002 PHE A 491 TRP 0.012 0.001 TRP A1074 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (13127) covalent geometry : angle 0.55486 / 0.31 (18351) hydrogen bonds : bond 0.04453 / 3.01 ( 595) hydrogen bonds : angle 4.32079 / 3.11 ( 1633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.450 Fit side-chains REVERT: A 220 ARG cc_start: 0.8902 (ttp-170) cc_final: 0.8640 (ttp-170) REVERT: A 235 ASN cc_start: 0.8488 (m-40) cc_final: 0.7681 (t0) REVERT: A 605 ASP cc_start: 0.8801 (t0) cc_final: 0.8233 (p0) REVERT: A 746 GLU cc_start: 0.8727 (tt0) cc_final: 0.8325 (tt0) REVERT: A 895 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6207 (tpt170) REVERT: A 919 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7584 (ttm170) REVERT: A 925 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6853 (mtm180) REVERT: A 947 ASP cc_start: 0.8524 (m-30) cc_final: 0.7918 (p0) REVERT: A 1108 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8797 (mt-10) REVERT: A 1194 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8761 (mp) outliers start: 36 outliers final: 22 residues processed: 130 average time/residue: 0.1073 time to fit residues: 20.8959 Evaluate side-chains 122 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 104 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.115192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077597 restraints weight = 25979.878| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.55 r_work: 0.2993 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13127 Z= 0.125 Angle : 0.498 11.438 18351 Z= 0.275 Chirality : 0.038 0.261 2167 Planarity : 0.003 0.046 1912 Dihedral : 20.527 179.836 3150 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.32 % Allowed : 19.14 % Favored : 77.54 % 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: -0.06 (0.23), residues: 1332 helix: 1.07 (0.20), residues: 681 sheet: -0.97 (0.46), residues: 131 loop : -1.24 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A 432 TRP 0.010 0.001 TRP A1074 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (13127) covalent geometry : angle 0.49804 / 0.27 (18351) hydrogen bonds : bond 0.03875 / 2.61 ( 595) hydrogen bonds : angle 4.20031 / 3.03 ( 1633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.477 Fit side-chains REVERT: A 220 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8632 (ttp-170) REVERT: A 235 ASN cc_start: 0.8485 (m-40) cc_final: 0.7676 (t0) REVERT: A 327 GLU cc_start: 0.8045 (pp20) cc_final: 0.7691 (pp20) REVERT: A 605 ASP cc_start: 0.8798 (t0) cc_final: 0.8216 (p0) REVERT: A 746 GLU cc_start: 0.8636 (tt0) cc_final: 0.8247 (tt0) REVERT: A 895 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6210 (tpt170) REVERT: A 919 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7589 (ttm170) REVERT: A 947 ASP cc_start: 0.8518 (m-30) cc_final: 0.7816 (p0) REVERT: A 1108 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8753 (mt-10) outliers start: 31 outliers final: 20 residues processed: 125 average time/residue: 0.1139 time to fit residues: 21.1369 Evaluate side-chains 116 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078154 restraints weight = 25847.489| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.54 r_work: 0.3002 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13127 Z= 0.119 Angle : 0.497 11.718 18351 Z= 0.275 Chirality : 0.038 0.263 2167 Planarity : 0.004 0.077 1912 Dihedral : 20.410 179.687 3150 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.99 % Allowed : 19.25 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1332 helix: 1.13 (0.20), residues: 685 sheet: -0.91 (0.46), residues: 131 loop : -1.20 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 395 TYR 0.016 0.001 TYR A 271 PHE 0.012 0.001 PHE A 491 TRP 0.008 0.001 TRP A1074 HIS 0.004 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (13127) covalent geometry : angle 0.49710 / 0.27 (18351) hydrogen bonds : bond 0.03761 / 2.54 ( 595) hydrogen bonds : angle 4.16534 / 3.02 ( 1633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.8626 (ttp-170) REVERT: A 235 ASN cc_start: 0.8510 (m-40) cc_final: 0.7677 (t0) REVERT: A 605 ASP cc_start: 0.8793 (t0) cc_final: 0.8212 (p0) REVERT: A 746 GLU cc_start: 0.8574 (tt0) cc_final: 0.8224 (tt0) REVERT: A 895 ARG cc_start: 0.6601 (mtp180) cc_final: 0.6214 (tpt170) REVERT: A 919 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7564 (ttm170) REVERT: A 925 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6954 (mtm180) REVERT: A 947 ASP cc_start: 0.8491 (m-30) cc_final: 0.7769 (p0) REVERT: A 1108 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8749 (mt-10) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.1076 time to fit residues: 19.5839 Evaluate side-chains 121 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 129 optimal weight: 0.0170 chunk 130 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.076673 restraints weight = 25704.537| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.53 r_work: 0.2978 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13127 Z= 0.158 Angle : 0.517 11.272 18351 Z= 0.284 Chirality : 0.039 0.264 2167 Planarity : 0.004 0.056 1912 Dihedral : 20.364 179.805 3150 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.78 % Allowed : 19.47 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1332 helix: 1.25 (0.21), residues: 673 sheet: -0.95 (0.46), residues: 131 loop : -1.07 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 215 TYR 0.021 0.001 TYR A 271 PHE 0.013 0.001 PHE A1235 TRP 0.012 0.001 TRP A1074 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (13127) covalent geometry : angle 0.51742 / 0.28 (18351) hydrogen bonds : bond 0.03913 / 2.65 ( 595) hydrogen bonds : angle 4.12022 / 2.97 ( 1633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: A 220 ARG cc_start: 0.8922 (ttp-170) cc_final: 0.8674 (ttp-170) REVERT: A 605 ASP cc_start: 0.8759 (t0) cc_final: 0.8197 (p0) REVERT: A 746 GLU cc_start: 0.8609 (tt0) cc_final: 0.8270 (tt0) REVERT: A 895 ARG cc_start: 0.6573 (mtp180) cc_final: 0.6170 (tpt170) REVERT: A 919 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7562 (ttm170) REVERT: A 925 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6695 (mtm180) REVERT: A 947 ASP cc_start: 0.8502 (m-30) cc_final: 0.7793 (p0) REVERT: A 1108 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8785 (mt-10) outliers start: 26 outliers final: 21 residues processed: 112 average time/residue: 0.1134 time to fit residues: 18.8988 Evaluate side-chains 114 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 925 ARG Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 HIS A 281 GLN A 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.115033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077631 restraints weight = 25860.179| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.53 r_work: 0.2992 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13127 Z= 0.131 Angle : 0.494 11.444 18351 Z= 0.272 Chirality : 0.038 0.269 2167 Planarity : 0.003 0.047 1912 Dihedral : 20.315 179.730 3150 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.25 % Allowed : 19.89 % Favored : 77.86 % 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: 0.25 (0.23), residues: 1332 helix: 1.32 (0.21), residues: 673 sheet: -0.93 (0.45), residues: 132 loop : -1.03 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.026 0.001 TYR A 271 PHE 0.013 0.001 PHE A 432 TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (13127) covalent geometry : angle 0.49431 / 0.27 (18351) hydrogen bonds : bond 0.03721 / 2.52 ( 595) hydrogen bonds : angle 4.05135 / 2.92 ( 1633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8910 (ttp-170) cc_final: 0.8643 (ttp-170) REVERT: A 605 ASP cc_start: 0.8775 (t0) cc_final: 0.8193 (p0) REVERT: A 746 GLU cc_start: 0.8558 (tt0) cc_final: 0.8180 (tt0) REVERT: A 895 ARG cc_start: 0.6575 (mtp180) cc_final: 0.6169 (tpt170) REVERT: A 919 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7557 (ttm170) REVERT: A 947 ASP cc_start: 0.8501 (m-30) cc_final: 0.7791 (p0) REVERT: A 1108 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8770 (mt-10) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.1092 time to fit residues: 17.7185 Evaluate side-chains 109 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 459 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** 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 = 0.3704 r_free = 0.3704 target = 0.111962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.074041 restraints weight = 26567.378| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.57 r_work: 0.2925 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13127 Z= 0.267 Angle : 0.599 10.844 18351 Z= 0.325 Chirality : 0.042 0.256 2167 Planarity : 0.004 0.064 1912 Dihedral : 20.368 177.949 3150 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % Favored : 77.43 % 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: 0.06 (0.23), residues: 1332 helix: 1.20 (0.21), residues: 668 sheet: -1.05 (0.45), residues: 131 loop : -1.14 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 215 TYR 0.026 0.002 TYR A 271 PHE 0.019 0.002 PHE A1235 TRP 0.014 0.002 TRP A1074 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (13127) covalent geometry : angle 0.59941 / 0.33 (18351) hydrogen bonds : bond 0.04649 / 3.15 ( 595) hydrogen bonds : angle 4.22325 / 3.01 ( 1633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.434 Fit side-chains REVERT: A 220 ARG cc_start: 0.8930 (ttp-170) cc_final: 0.8637 (ttp-170) REVERT: A 605 ASP cc_start: 0.8829 (t0) cc_final: 0.8253 (p0) REVERT: A 746 GLU cc_start: 0.8750 (tt0) cc_final: 0.8329 (tt0) REVERT: A 895 ARG cc_start: 0.6567 (mtp180) cc_final: 0.6151 (tpt170) REVERT: A 919 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7644 (ttm170) REVERT: A 947 ASP cc_start: 0.8515 (m-30) cc_final: 0.7845 (p0) REVERT: A 1108 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8838 (mt-10) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.1051 time to fit residues: 17.2407 Evaluate side-chains 107 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 54 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.114625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076997 restraints weight = 26317.916| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.53 r_work: 0.2982 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13127 Z= 0.118 Angle : 0.505 11.350 18351 Z= 0.278 Chirality : 0.038 0.270 2167 Planarity : 0.003 0.044 1912 Dihedral : 20.333 178.652 3150 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.71 % Allowed : 20.53 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1332 helix: 1.35 (0.21), residues: 674 sheet: -1.03 (0.46), residues: 131 loop : -1.05 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 215 TYR 0.025 0.001 TYR A 271 PHE 0.013 0.001 PHE A 432 TRP 0.008 0.001 TRP A 464 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (13127) covalent geometry : angle 0.50500 / 0.28 (18351) hydrogen bonds : bond 0.03761 / 2.55 ( 595) hydrogen bonds : angle 4.07552 / 2.93 ( 1633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.67 seconds wall clock time: 55 minutes 14.13 seconds (3314.13 seconds total)