Starting phenix.real_space_refine on Fri Sep 11 23:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.cif" model { file = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0z_0585/09_2026/6o0z_0585.cif" } resolution = 3.3 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= 0.043 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 134 5.49 5 S 15 5.16 5 C 7080 2.51 5 N 2132 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9063 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1288, 9063 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 391} Link IDs: {'PTRANS': 34, 'TRANS': 1253} Chain breaks: 11 Unresolved non-hydrogen bonds: 1545 Unresolved non-hydrogen angles: 1919 Unresolved non-hydrogen dihedrals: 1252 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 61, 'PHE:plan': 16, 'GLN:plan1': 25, 'ASN:plan1': 32, 'ARG:plan': 26, 'TYR:plan': 12, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 883 Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2058 Classifications: {'RNAv2': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 84} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 563 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 228 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 2.85, per 1000 atoms: 0.24 Number of scatterers: 11912 At special positions: 0 Unit cell: (140.448, 127.072, 98.648, 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 15 16.00 P 134 15.00 O 2551 8.00 N 2132 7.00 C 7080 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: 1.10 Conformation dependent library (CDL) restraints added in 506.0 milliseconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 52.7% alpha, 6.3% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.960A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.018A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.608A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.592A pdb=" N ILE A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.594A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.557A 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 removed outlier: 3.520A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) 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 395 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.352A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.628A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.572A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.618A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.676A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 543 through 556 removed outlier: 4.275A pdb=" N ALA A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.524A pdb=" N ASP A 608 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 609 " --> pdb=" O PHE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 605 through 609' Processing helix chain 'A' and resid 610 through 626 removed outlier: 4.013A pdb=" N ASP A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.602A pdb=" N SER A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.690A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.798A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.545A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 removed outlier: 3.562A pdb=" N GLY A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.974A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.857A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.131A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.870A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.747A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.690A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 4.029A 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 removed outlier: 3.592A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.906A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1302 through 1312 removed outlier: 4.172A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1341 through 1344 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.201A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (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: 6.251A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.760A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 1.38 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: 2133 1.33 - 1.45: 3597 1.45 - 1.57: 6375 1.57 - 1.69: 266 1.69 - 1.81: 28 Bond restraints: 12399 Sorted by residual: bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" C3' DC C 27 " pdb=" C2' DC C 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C4' DT C 19 " pdb=" C3' DT C 19 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.55e+00 bond pdb=" C3' DT D 31 " pdb=" O3' DT D 31 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" C3' DT D 37 " pdb=" C2' DT D 37 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.25e+00 ... (remaining 12394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16485 1.65 - 3.30: 832 3.30 - 4.95: 121 4.95 - 6.60: 24 6.60 - 8.25: 9 Bond angle restraints: 17471 Sorted by residual: angle pdb=" C3' A B 68 " pdb=" O3' A B 68 " pdb=" P A B 69 " ideal model delta sigma weight residual 119.70 126.75 -7.05 1.20e+00 6.94e-01 3.45e+01 angle pdb=" O4' DC C 17 " pdb=" C4' DC C 17 " pdb=" C3' DC C 17 " ideal model delta sigma weight residual 106.00 102.70 3.30 6.00e-01 2.78e+00 3.02e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 119.70 125.37 -5.67 1.20e+00 6.94e-01 2.23e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 17466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 6701 34.56 - 69.13: 376 69.13 - 103.69: 16 103.69 - 138.25: 0 138.25 - 172.81: 2 Dihedral angle restraints: 7095 sinusoidal: 3318 harmonic: 3777 Sorted by residual: dihedral pdb=" C4' A B 88 " pdb=" C3' A B 88 " pdb=" C2' A B 88 " pdb=" C1' A B 88 " ideal model delta sinusoidal sigma weight residual 36.34 -37.39 73.73 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' G B 89 " pdb=" C3' G B 89 " pdb=" C2' G B 89 " pdb=" C1' G B 89 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.73 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' C B 55 " pdb=" C3' C B 55 " pdb=" C2' C B 55 " pdb=" C1' C B 55 " ideal model delta sinusoidal sigma weight residual 36.34 -36.18 72.52 1 3.10e+00 1.04e-01 6.99e+02 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1736 0.066 - 0.132: 251 0.132 - 0.198: 30 0.198 - 0.264: 91 0.264 - 0.330: 20 Chirality restraints: 2128 Sorted by residual: 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 -2.50 -2.17 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" P G B 43 " pdb=" OP1 G B 43 " pdb=" OP2 G B 43 " pdb=" O5' G B 43 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' C B 55 " pdb=" C3' C B 55 " pdb=" O2' C B 55 " pdb=" C1' C B 55 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2125 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 474 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 475 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A1229 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1342 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL A1342 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A1342 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A1343 " -0.011 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3643 2.82 - 3.34: 9736 3.34 - 3.86: 20451 3.86 - 4.38: 21925 4.38 - 4.90: 35065 Nonbonded interactions: 90820 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.302 3.040 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.308 3.040 nonbonded pdb=" O LYS A 141 " pdb=" OG SER A 145 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A1109 " pdb=" OP2 DG C 11 " model vdw 2.334 3.040 nonbonded pdb=" N2 G B 73 " pdb=" OP2 A B 76 " model vdw 2.337 3.120 ... (remaining 90815 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=0.49 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 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 : 0.006 0.067 12399 Z= 0.353 Angle : 0.833 8.255 17471 Z= 0.482 Chirality : 0.071 0.330 2128 Planarity : 0.005 0.052 1752 Dihedral : 18.095 172.814 4635 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.27 % Allowed : 8.34 % Favored : 91.38 % 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: -4.11 (0.18), residues: 1264 helix: -2.68 (0.15), residues: 608 sheet: -0.72 (0.46), residues: 127 loop : -3.20 (0.21), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1084 TYR 0.014 0.002 TYR A 325 PHE 0.016 0.002 PHE A1324 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.35 (12399) covalent geometry : angle 0.83306 / 0.48 (17471) hydrogen bonds : bond 0.13168 / 9.06 ( 563) hydrogen bonds : angle 6.24808 / 4.76 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.377 Fit side-chains REVERT: A 518 PHE cc_start: 0.9042 (t80) cc_final: 0.8744 (t80) REVERT: A 927 ILE cc_start: 0.9262 (mt) cc_final: 0.9034 (tp) REVERT: A 933 GLN cc_start: 0.9239 (tt0) cc_final: 0.9036 (tm-30) REVERT: A 961 LYS cc_start: 0.8817 (tptp) cc_final: 0.8564 (tptp) REVERT: A 1183 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8333 (tm-30) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1173 time to fit residues: 11.9975 Evaluate side-chains 52 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1098 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 113 HIS A 342 GLN A 420 HIS A 426 GLN A 990 ASN A1272 GLN A1308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057029 restraints weight = 36499.021| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.01 r_work: 0.2701 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12399 Z= 0.272 Angle : 0.979 19.516 17471 Z= 0.440 Chirality : 0.088 1.342 2128 Planarity : 0.004 0.061 1752 Dihedral : 17.523 175.280 2926 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.23 % Allowed : 11.90 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.21), residues: 1264 helix: -0.79 (0.19), residues: 625 sheet: -0.18 (0.53), residues: 105 loop : -2.92 (0.23), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 976 TYR 0.014 0.001 TYR A 325 PHE 0.009 0.001 PHE A 432 TRP 0.016 0.002 TRP A1074 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.27 (12399) covalent geometry : angle 0.97907 / 0.44 (17471) hydrogen bonds : bond 0.05280 / 3.80 ( 563) hydrogen bonds : angle 4.67897 / 3.56 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.510 Fit side-chains REVERT: A 927 ILE cc_start: 0.9248 (mt) cc_final: 0.8937 (tp) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.0899 time to fit residues: 9.0616 Evaluate side-chains 51 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.087474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058365 restraints weight = 36975.774| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.99 r_work: 0.2755 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12399 Z= 0.183 Angle : 0.760 15.526 17471 Z= 0.351 Chirality : 0.063 0.806 2128 Planarity : 0.003 0.058 1752 Dihedral : 17.590 173.501 2926 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.23 % Allowed : 12.59 % Favored : 86.18 % 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: -1.50 (0.23), residues: 1264 helix: 0.14 (0.21), residues: 621 sheet: -0.47 (0.51), residues: 115 loop : -2.56 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 976 TYR 0.010 0.001 TYR A 325 PHE 0.008 0.001 PHE A 478 TRP 0.011 0.001 TRP A1074 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (12399) covalent geometry : angle 0.75958 / 0.35 (17471) hydrogen bonds : bond 0.04570 / 3.31 ( 563) hydrogen bonds : angle 4.28625 / 3.25 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.429 Fit side-chains REVERT: A 927 ILE cc_start: 0.9252 (mt) cc_final: 0.9007 (tp) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.0887 time to fit residues: 8.5376 Evaluate side-chains 57 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 128 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 723 HIS A 990 ASN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.086379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057644 restraints weight = 36572.892| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.94 r_work: 0.2730 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12399 Z= 0.215 Angle : 0.744 13.392 17471 Z= 0.345 Chirality : 0.058 0.636 2128 Planarity : 0.003 0.058 1752 Dihedral : 17.712 169.774 2926 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.05 % Allowed : 13.54 % Favored : 84.40 % 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: -1.01 (0.24), residues: 1264 helix: 0.67 (0.22), residues: 616 sheet: -0.62 (0.47), residues: 137 loop : -2.42 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.010 0.001 TYR A 325 PHE 0.009 0.001 PHE A 518 TRP 0.012 0.001 TRP A1074 HIS 0.003 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (12399) covalent geometry : angle 0.74369 / 0.35 (17471) hydrogen bonds : bond 0.04719 / 3.43 ( 563) hydrogen bonds : angle 4.19065 / 3.17 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.490 Fit side-chains REVERT: A 927 ILE cc_start: 0.9296 (mt) cc_final: 0.9044 (tp) REVERT: A 1169 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mtp) outliers start: 15 outliers final: 12 residues processed: 62 average time/residue: 0.0916 time to fit residues: 9.3258 Evaluate side-chains 60 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 57 optimal weight: 40.0000 chunk 2 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.087496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058458 restraints weight = 36952.489| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.98 r_work: 0.2758 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12399 Z= 0.164 Angle : 0.681 10.577 17471 Z= 0.320 Chirality : 0.055 0.506 2128 Planarity : 0.003 0.057 1752 Dihedral : 17.616 168.732 2926 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.64 % Allowed : 14.91 % Favored : 83.45 % 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: -0.61 (0.24), residues: 1264 helix: 1.04 (0.22), residues: 610 sheet: -0.45 (0.48), residues: 137 loop : -2.24 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.012 0.001 TYR A 271 PHE 0.010 0.001 PHE A 432 TRP 0.008 0.001 TRP A1074 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (12399) covalent geometry : angle 0.68079 / 0.32 (17471) hydrogen bonds : bond 0.04301 / 3.13 ( 563) hydrogen bonds : angle 4.03611 / 3.06 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.359 Fit side-chains REVERT: A 927 ILE cc_start: 0.9261 (mt) cc_final: 0.9018 (tp) REVERT: A 1169 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7740 (mtp) outliers start: 12 outliers final: 11 residues processed: 59 average time/residue: 0.0890 time to fit residues: 8.5359 Evaluate side-chains 60 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.086294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057289 restraints weight = 36933.324| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.92 r_work: 0.2726 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12399 Z= 0.228 Angle : 0.717 11.537 17471 Z= 0.335 Chirality : 0.055 0.504 2128 Planarity : 0.003 0.058 1752 Dihedral : 17.601 167.246 2926 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.46 % Allowed : 14.91 % Favored : 82.63 % 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: -0.55 (0.24), residues: 1264 helix: 1.10 (0.22), residues: 617 sheet: -0.43 (0.48), residues: 137 loop : -2.26 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.013 0.001 TYR A 325 PHE 0.009 0.001 PHE A 432 TRP 0.008 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (12399) covalent geometry : angle 0.71656 / 0.34 (17471) hydrogen bonds : bond 0.04700 / 3.42 ( 563) hydrogen bonds : angle 4.08902 / 3.10 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.405 Fit side-chains REVERT: A 927 ILE cc_start: 0.9303 (mt) cc_final: 0.9056 (tp) REVERT: A 1169 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7900 (mtp) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 0.0882 time to fit residues: 9.5719 Evaluate side-chains 61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.086149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.057372 restraints weight = 36405.760| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.91 r_work: 0.2726 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12399 Z= 0.229 Angle : 0.721 11.140 17471 Z= 0.339 Chirality : 0.055 0.527 2128 Planarity : 0.003 0.057 1752 Dihedral : 17.507 166.398 2926 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.60 % Allowed : 15.32 % Favored : 82.08 % 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: -0.45 (0.24), residues: 1264 helix: 1.20 (0.22), residues: 617 sheet: -0.44 (0.48), residues: 137 loop : -2.23 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.013 0.001 TYR A 325 PHE 0.010 0.001 PHE A 432 TRP 0.007 0.001 TRP A1074 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (12399) covalent geometry : angle 0.72084 / 0.34 (17471) hydrogen bonds : bond 0.04792 / 3.49 ( 563) hydrogen bonds : angle 4.09154 / 3.10 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.389 Fit side-chains REVERT: A 927 ILE cc_start: 0.9317 (mt) cc_final: 0.9077 (tp) REVERT: A 1169 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7900 (mtp) outliers start: 19 outliers final: 15 residues processed: 64 average time/residue: 0.0891 time to fit residues: 9.3840 Evaluate side-chains 63 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.086809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.058047 restraints weight = 36531.922| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.92 r_work: 0.2745 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12399 Z= 0.176 Angle : 0.684 10.174 17471 Z= 0.322 Chirality : 0.053 0.508 2128 Planarity : 0.003 0.054 1752 Dihedral : 17.371 166.555 2926 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.19 % Allowed : 15.87 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1264 helix: 1.36 (0.22), residues: 610 sheet: -0.34 (0.48), residues: 137 loop : -2.13 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.011 0.001 TYR A 271 PHE 0.010 0.001 PHE A 432 TRP 0.010 0.001 TRP A1074 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (12399) covalent geometry : angle 0.68399 / 0.32 (17471) hydrogen bonds : bond 0.04452 / 3.24 ( 563) hydrogen bonds : angle 3.98804 / 3.02 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.389 Fit side-chains REVERT: A 927 ILE cc_start: 0.9283 (mt) cc_final: 0.9034 (tp) REVERT: A 1169 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7802 (mtp) outliers start: 16 outliers final: 13 residues processed: 63 average time/residue: 0.0882 time to fit residues: 9.0898 Evaluate side-chains 61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 41 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.085946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057215 restraints weight = 36572.998| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.91 r_work: 0.2719 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12399 Z= 0.245 Angle : 0.733 11.075 17471 Z= 0.344 Chirality : 0.055 0.523 2128 Planarity : 0.003 0.056 1752 Dihedral : 17.348 165.731 2926 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.46 % Allowed : 15.18 % Favored : 82.35 % 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 (0.25), residues: 1264 helix: 1.29 (0.22), residues: 616 sheet: -0.38 (0.48), residues: 137 loop : -2.19 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.014 0.001 TYR A 325 PHE 0.021 0.001 PHE A 518 TRP 0.010 0.001 TRP A1074 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.25 (12399) covalent geometry : angle 0.73263 / 0.34 (17471) hydrogen bonds : bond 0.04873 / 3.54 ( 563) hydrogen bonds : angle 4.07948 / 3.09 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.334 Fit side-chains REVERT: A 927 ILE cc_start: 0.9325 (mt) cc_final: 0.9092 (tp) REVERT: A 1089 MET cc_start: 0.9176 (ttt) cc_final: 0.8946 (ttm) REVERT: A 1169 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7947 (mtp) outliers start: 18 outliers final: 14 residues processed: 64 average time/residue: 0.0869 time to fit residues: 8.9960 Evaluate side-chains 62 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 25 optimal weight: 50.0000 chunk 118 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058553 restraints weight = 36717.638| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.93 r_work: 0.2751 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12399 Z= 0.153 Angle : 0.670 9.807 17471 Z= 0.316 Chirality : 0.052 0.497 2128 Planarity : 0.003 0.054 1752 Dihedral : 17.251 166.508 2926 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.92 % Allowed : 15.73 % Favored : 82.35 % 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: -0.13 (0.25), residues: 1264 helix: 1.46 (0.22), residues: 613 sheet: -0.23 (0.49), residues: 136 loop : -2.04 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.011 0.001 TYR A 271 PHE 0.011 0.001 PHE A 432 TRP 0.007 0.001 TRP A1074 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (12399) covalent geometry : angle 0.67003 / 0.32 (17471) hydrogen bonds : bond 0.04282 / 3.12 ( 563) hydrogen bonds : angle 3.91493 / 2.96 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.431 Fit side-chains REVERT: A 927 ILE cc_start: 0.9273 (mt) cc_final: 0.9036 (tp) REVERT: A 1169 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: A 1183 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8960 (tm-30) outliers start: 14 outliers final: 13 residues processed: 64 average time/residue: 0.0836 time to fit residues: 8.7261 Evaluate side-chains 61 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 109 optimal weight: 0.0980 chunk 114 optimal weight: 8.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059023 restraints weight = 36778.624| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.98 r_work: 0.2773 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12399 Z= 0.148 Angle : 0.663 10.447 17471 Z= 0.312 Chirality : 0.051 0.457 2128 Planarity : 0.003 0.053 1752 Dihedral : 17.199 166.562 2926 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.92 % Allowed : 15.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1264 helix: 1.61 (0.22), residues: 613 sheet: -0.13 (0.49), residues: 136 loop : -1.97 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.011 0.001 TYR A 325 PHE 0.021 0.001 PHE A 518 TRP 0.008 0.001 TRP A1074 HIS 0.002 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (12399) covalent geometry : angle 0.66265 / 0.31 (17471) hydrogen bonds : bond 0.04059 / 2.95 ( 563) hydrogen bonds : angle 3.81384 / 2.89 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3014.35 seconds wall clock time: 52 minutes 21.08 seconds (3141.08 seconds total)