Starting phenix.real_space_refine on Wed Aug 5 16:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t77_41086/08_2026/8t77_41086.map" } resolution = 3.25 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= 0.008 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 114 5.49 5 S 16 5.16 5 C 6427 2.51 5 N 1889 2.21 5 O 2299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8328 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 27, 'TRANS': 997} Chain breaks: 8 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1905 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 2.07, per 1000 atoms: 0.19 Number of scatterers: 10745 At special positions: 0 Unit cell: (85.8196, 120.814, 122.48, 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 16 16.00 P 114 15.00 O 2299 8.00 N 1889 7.00 C 6427 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: 0.87 Conformation dependent library (CDL) restraints added in 461.9 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 55.7% alpha, 7.3% beta 35 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.650A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.828A 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 181 through 196 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.585A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (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 removed outlier: 3.568A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.187A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.192A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.597A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.615A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.999A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.274A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.743A 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 removed outlier: 4.135A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.526A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 removed outlier: 3.603A pdb=" N LYS A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.701A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.151A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.008A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.893A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.663A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.738A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 999 removed outlier: 4.776A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.501A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.819A 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 1240 removed outlier: 3.831A pdb=" N SER A1240 " --> pdb=" O LEU A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1246 Processing helix chain 'A' and resid 1251 through 1261 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.676A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.655A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 8 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 49 " --> pdb=" O TRP A 18 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.174A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.924A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1325 360 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.17 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: 2297 1.33 - 1.45: 2911 1.45 - 1.57: 5718 1.57 - 1.69: 226 1.69 - 1.81: 30 Bond restraints: 11182 Sorted by residual: bond pdb=" C5' DA D 45 " pdb=" C4' DA D 45 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.24e+01 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT C 13 " pdb=" C2' DT C 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C1' DT C 13 " pdb=" N1 DT C 13 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.44e+00 bond pdb=" C3' DC D 39 " pdb=" C2' DC D 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.23e+00 ... (remaining 11177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 15328 3.20 - 6.40: 234 6.40 - 9.61: 28 9.61 - 12.81: 8 12.81 - 16.01: 2 Bond angle restraints: 15600 Sorted by residual: angle pdb=" C2 C B 18 " pdb=" N1 C B 18 " pdb=" C6 C B 18 " ideal model delta sigma weight residual 120.30 116.65 3.65 4.00e-01 6.25e+00 8.32e+01 angle pdb=" N1 C B 18 " pdb=" C6 C B 18 " pdb=" C5 C B 18 " ideal model delta sigma weight residual 121.00 125.54 -4.54 5.00e-01 4.00e+00 8.24e+01 angle pdb=" O4' DC D 44 " pdb=" C1' DC D 44 " pdb=" N1 DC D 44 " ideal model delta sigma weight residual 108.00 112.89 -4.89 7.00e-01 2.04e+00 4.88e+01 angle pdb=" O5' C B 18 " pdb=" C5' C B 18 " pdb=" C4' C B 18 " ideal model delta sigma weight residual 109.40 114.93 -5.53 8.00e-01 1.56e+00 4.77e+01 angle pdb=" O5' DC D 44 " pdb=" C5' DC D 44 " pdb=" C4' DC D 44 " ideal model delta sigma weight residual 109.40 114.81 -5.41 8.00e-01 1.56e+00 4.57e+01 ... (remaining 15595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 6266 30.44 - 60.88: 452 60.88 - 91.32: 79 91.32 - 121.77: 3 121.77 - 152.21: 2 Dihedral angle restraints: 6802 sinusoidal: 3786 harmonic: 3016 Sorted by residual: dihedral pdb=" CA TRP A 464 " pdb=" C TRP A 464 " pdb=" N MET A 465 " pdb=" CA MET A 465 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LYS A1107 " pdb=" C LYS A1107 " pdb=" N GLU A1108 " pdb=" CA GLU A1108 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A1259 " pdb=" C VAL A1259 " pdb=" N GLU A1260 " pdb=" CA GLU A1260 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1495 0.078 - 0.155: 297 0.155 - 0.233: 20 0.233 - 0.310: 5 0.310 - 0.388: 3 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB ILE A1352 " pdb=" CA ILE A1352 " pdb=" CG1 ILE A1352 " pdb=" CG2 ILE A1352 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CG LEU A 597 " pdb=" CB LEU A 597 " pdb=" CD1 LEU A 597 " pdb=" CD2 LEU A 597 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.66 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1817 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 19 " -0.022 2.00e-02 2.50e+03 2.40e-02 1.73e+01 pdb=" N9 G B 19 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G B 19 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 19 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 19 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G B 19 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G B 19 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G B 19 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 19 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1276 " 0.024 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE A1276 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A1276 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1276 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A1276 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1276 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A1276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " 0.023 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR A 517 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.007 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 442 2.70 - 3.25: 10213 3.25 - 3.80: 18734 3.80 - 4.35: 23697 4.35 - 4.90: 35637 Nonbonded interactions: 88723 Sorted by model distance: nonbonded pdb=" O GLY A 736 " pdb=" OG1 THR A 740 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP A1267 " pdb=" OH TYR A1294 " model vdw 2.245 3.040 nonbonded pdb=" O LEU A 455 " pdb=" O2' G B 58 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR A1102 " pdb=" OP2 U B 64 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.295 3.040 ... (remaining 88718 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=0.00 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: 5.060 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.200 Find NCS groups from input model: 0.040 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.055 11182 Z= 0.307 Angle : 1.050 16.010 15600 Z= 0.685 Chirality : 0.062 0.388 1820 Planarity : 0.007 0.082 1561 Dihedral : 19.381 152.208 4842 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 21.18 % Favored : 78.05 % 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: -1.56 (0.24), residues: 1008 helix: -1.21 (0.20), residues: 502 sheet: -0.24 (0.51), residues: 110 loop : -0.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1111 TYR 0.068 0.004 TYR A 517 PHE 0.068 0.003 PHE A1276 TRP 0.059 0.005 TRP A 18 HIS 0.015 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.31 (11182) covalent geometry : angle 1.04969 / 0.68 (15600) hydrogen bonds : bond 0.16346 / 10.80 ( 447) hydrogen bonds : angle 6.52391 / 4.62 ( 1223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.9085 (mt0) cc_final: 0.8484 (mm-40) REVERT: A 397 ASP cc_start: 0.7808 (t0) cc_final: 0.7533 (t0) REVERT: A 482 VAL cc_start: 0.9068 (t) cc_final: 0.8757 (p) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.0906 time to fit residues: 11.3093 Evaluate side-chains 75 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 612 ASN A 650 GLN A1349 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.091378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.067691 restraints weight = 42610.245| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.52 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11182 Z= 0.260 Angle : 0.725 9.632 15600 Z= 0.392 Chirality : 0.045 0.257 1820 Planarity : 0.005 0.037 1561 Dihedral : 19.937 154.419 2729 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.99 % Allowed : 18.07 % Favored : 78.94 % 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: -0.75 (0.25), residues: 1008 helix: -0.13 (0.22), residues: 516 sheet: -0.72 (0.52), residues: 101 loop : -0.73 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 654 TYR 0.026 0.002 TYR A 362 PHE 0.015 0.002 PHE A 966 TRP 0.025 0.003 TRP A 18 HIS 0.007 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (11182) covalent geometry : angle 0.72508 / 0.39 (15600) hydrogen bonds : bond 0.06107 / 4.09 ( 447) hydrogen bonds : angle 5.21668 / 3.71 ( 1223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 MET cc_start: 0.5018 (ttm) cc_final: 0.4766 (ttm) REVERT: A 397 ASP cc_start: 0.8043 (t0) cc_final: 0.7774 (t0) REVERT: A 495 MET cc_start: 0.7652 (mmm) cc_final: 0.7432 (mmp) REVERT: A 738 LEU cc_start: 0.8438 (mp) cc_final: 0.8237 (tt) REVERT: A 1337 ARG cc_start: 0.7019 (tpt90) cc_final: 0.6806 (tpt90) outliers start: 27 outliers final: 17 residues processed: 88 average time/residue: 0.0870 time to fit residues: 11.7190 Evaluate side-chains 78 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 1093 ASN Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 489 GLN A1305 GLN A1335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.093538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.069822 restraints weight = 42101.183| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.63 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11182 Z= 0.120 Angle : 0.561 10.098 15600 Z= 0.309 Chirality : 0.039 0.262 1820 Planarity : 0.004 0.034 1561 Dihedral : 19.846 152.621 2727 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.99 % Allowed : 18.07 % Favored : 78.94 % 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: -0.37 (0.25), residues: 1008 helix: 0.21 (0.22), residues: 515 sheet: -0.39 (0.53), residues: 101 loop : -0.65 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.027 0.002 TYR A 988 PHE 0.018 0.002 PHE A 966 TRP 0.015 0.002 TRP A 18 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11182) covalent geometry : angle 0.56095 / 0.31 (15600) hydrogen bonds : bond 0.04664 / 3.12 ( 447) hydrogen bonds : angle 4.79203 / 3.44 ( 1223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8133 (t0) cc_final: 0.7868 (t0) REVERT: A 495 MET cc_start: 0.7648 (mmm) cc_final: 0.7391 (mmp) REVERT: A 961 LYS cc_start: 0.9259 (mttt) cc_final: 0.8990 (mppt) REVERT: A 1337 ARG cc_start: 0.6887 (tpt90) cc_final: 0.6604 (tpt90) outliers start: 27 outliers final: 12 residues processed: 94 average time/residue: 0.1013 time to fit residues: 14.0504 Evaluate side-chains 77 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1254 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 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 = 0.4087 r_free = 0.4087 target = 0.091941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.068087 restraints weight = 42421.111| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.48 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11182 Z= 0.156 Angle : 0.573 9.052 15600 Z= 0.313 Chirality : 0.040 0.266 1820 Planarity : 0.004 0.034 1561 Dihedral : 19.709 152.654 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.88 % Allowed : 18.29 % 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: -0.26 (0.25), residues: 1008 helix: 0.43 (0.23), residues: 516 sheet: -0.37 (0.53), residues: 96 loop : -0.80 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.016 0.002 TYR A 450 PHE 0.044 0.002 PHE A1258 TRP 0.010 0.001 TRP A1136 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (11182) covalent geometry : angle 0.57281 / 0.31 (15600) hydrogen bonds : bond 0.04872 / 3.25 ( 447) hydrogen bonds : angle 4.62662 / 3.32 ( 1223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.9015 (tp) cc_final: 0.8710 (tt) REVERT: A 397 ASP cc_start: 0.8188 (t0) cc_final: 0.7933 (t0) REVERT: A 495 MET cc_start: 0.7710 (mmm) cc_final: 0.7395 (mmp) REVERT: A 961 LYS cc_start: 0.9269 (mttt) cc_final: 0.8992 (mppt) REVERT: A 1276 PHE cc_start: 0.8816 (t80) cc_final: 0.8558 (t80) REVERT: A 1337 ARG cc_start: 0.6862 (tpt90) cc_final: 0.6522 (tpt90) outliers start: 26 outliers final: 19 residues processed: 90 average time/residue: 0.0939 time to fit residues: 12.7116 Evaluate side-chains 85 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 84 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS ** A1305 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 = 0.4106 r_free = 0.4106 target = 0.092831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.069219 restraints weight = 41678.488| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.43 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11182 Z= 0.114 Angle : 0.537 9.259 15600 Z= 0.293 Chirality : 0.039 0.358 1820 Planarity : 0.003 0.048 1561 Dihedral : 19.650 151.426 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.99 % Allowed : 18.51 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1008 helix: 0.49 (0.23), residues: 515 sheet: -0.26 (0.54), residues: 96 loop : -0.71 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.027 0.002 TYR A 988 PHE 0.046 0.002 PHE A1258 TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (11182) covalent geometry : angle 0.53745 / 0.29 (15600) hydrogen bonds : bond 0.04250 / 2.83 ( 447) hydrogen bonds : angle 4.49232 / 3.24 ( 1223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8993 (tp) cc_final: 0.8673 (tt) REVERT: A 397 ASP cc_start: 0.8235 (t0) cc_final: 0.7969 (t0) REVERT: A 601 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (tt) REVERT: A 961 LYS cc_start: 0.9262 (mttt) cc_final: 0.8988 (mppt) REVERT: A 1099 GLU cc_start: 0.8487 (pm20) cc_final: 0.8149 (pm20) REVERT: A 1276 PHE cc_start: 0.8812 (t80) cc_final: 0.8562 (t80) REVERT: A 1326 TYR cc_start: 0.7318 (t80) cc_final: 0.7108 (t80) REVERT: A 1337 ARG cc_start: 0.6821 (tpt90) cc_final: 0.6447 (tpt90) outliers start: 27 outliers final: 15 residues processed: 87 average time/residue: 0.0958 time to fit residues: 12.3208 Evaluate side-chains 82 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.090168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.066013 restraints weight = 43273.524| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.54 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11182 Z= 0.174 Angle : 0.572 9.325 15600 Z= 0.310 Chirality : 0.039 0.244 1820 Planarity : 0.004 0.046 1561 Dihedral : 19.576 152.703 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 19.29 % Favored : 78.16 % 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: -0.22 (0.26), residues: 1008 helix: 0.50 (0.23), residues: 518 sheet: -0.27 (0.55), residues: 96 loop : -0.87 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 654 TYR 0.018 0.002 TYR A 988 PHE 0.036 0.002 PHE A1258 TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11182) covalent geometry : angle 0.57235 / 0.31 (15600) hydrogen bonds : bond 0.04820 / 3.23 ( 447) hydrogen bonds : angle 4.50871 / 3.23 ( 1223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8386 (t0) cc_final: 0.8130 (t0) REVERT: A 601 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 961 LYS cc_start: 0.9264 (mttt) cc_final: 0.8980 (mppt) REVERT: A 1099 GLU cc_start: 0.8559 (pm20) cc_final: 0.8292 (pm20) REVERT: A 1337 ARG cc_start: 0.6867 (tpt90) cc_final: 0.6428 (tpt90) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.1009 time to fit residues: 12.1285 Evaluate side-chains 80 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.091161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.067453 restraints weight = 41737.515| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.40 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11182 Z= 0.118 Angle : 0.530 8.941 15600 Z= 0.288 Chirality : 0.038 0.250 1820 Planarity : 0.003 0.043 1561 Dihedral : 19.567 151.455 2727 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.33 % Allowed : 18.74 % Favored : 77.94 % 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: -0.09 (0.26), residues: 1008 helix: 0.60 (0.23), residues: 516 sheet: -0.20 (0.56), residues: 96 loop : -0.78 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.037 0.002 TYR A 988 PHE 0.036 0.002 PHE A1258 TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (11182) covalent geometry : angle 0.52989 / 0.29 (15600) hydrogen bonds : bond 0.04050 / 2.71 ( 447) hydrogen bonds : angle 4.33712 / 3.12 ( 1223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8382 (t0) cc_final: 0.8141 (t0) REVERT: A 601 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 958 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7733 (tp) REVERT: A 961 LYS cc_start: 0.9251 (mttt) cc_final: 0.8963 (mppt) REVERT: A 1099 GLU cc_start: 0.8534 (pm20) cc_final: 0.8260 (pm20) REVERT: A 1208 ASN cc_start: 0.9179 (t0) cc_final: 0.8942 (t0) REVERT: A 1276 PHE cc_start: 0.8880 (t80) cc_final: 0.8613 (t80) REVERT: A 1337 ARG cc_start: 0.6850 (tpt90) cc_final: 0.6387 (tpt90) outliers start: 30 outliers final: 18 residues processed: 86 average time/residue: 0.0897 time to fit residues: 11.5274 Evaluate side-chains 84 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.090759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.066924 restraints weight = 42825.240| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.45 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11182 Z= 0.129 Angle : 0.539 8.584 15600 Z= 0.290 Chirality : 0.038 0.331 1820 Planarity : 0.003 0.040 1561 Dihedral : 19.494 151.369 2727 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.10 % Allowed : 18.74 % Favored : 78.16 % 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: -0.09 (0.26), residues: 1008 helix: 0.62 (0.23), residues: 516 sheet: -0.23 (0.56), residues: 96 loop : -0.82 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 494 TYR 0.021 0.002 TYR A 988 PHE 0.032 0.002 PHE A1258 TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11182) covalent geometry : angle 0.53856 / 0.29 (15600) hydrogen bonds : bond 0.04204 / 2.80 ( 447) hydrogen bonds : angle 4.34768 / 3.12 ( 1223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8401 (t0) cc_final: 0.8171 (t0) REVERT: A 601 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8821 (tt) REVERT: A 958 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 961 LYS cc_start: 0.9275 (mttt) cc_final: 0.8988 (mppt) REVERT: A 1099 GLU cc_start: 0.8504 (pm20) cc_final: 0.8200 (pm20) REVERT: A 1208 ASN cc_start: 0.9184 (t0) cc_final: 0.8902 (t0) REVERT: A 1276 PHE cc_start: 0.8890 (t80) cc_final: 0.8578 (t80) REVERT: A 1337 ARG cc_start: 0.6856 (tpt90) cc_final: 0.6350 (tpt90) outliers start: 28 outliers final: 23 residues processed: 84 average time/residue: 0.1042 time to fit residues: 12.9110 Evaluate side-chains 88 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.091636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.068156 restraints weight = 46225.932| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 4.43 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11182 Z= 0.178 Angle : 0.577 8.200 15600 Z= 0.313 Chirality : 0.040 0.244 1820 Planarity : 0.004 0.038 1561 Dihedral : 19.546 152.662 2727 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.99 % Allowed : 19.73 % Favored : 77.27 % 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: -0.12 (0.26), residues: 1008 helix: 0.67 (0.23), residues: 517 sheet: -0.35 (0.56), residues: 96 loop : -0.92 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 654 TYR 0.033 0.002 TYR A 988 PHE 0.050 0.002 PHE A 518 TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (11182) covalent geometry : angle 0.57665 / 0.31 (15600) hydrogen bonds : bond 0.04682 / 3.13 ( 447) hydrogen bonds : angle 4.42859 / 3.17 ( 1223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8987 (mtm110) cc_final: 0.8694 (ttm-80) REVERT: A 601 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8857 (tt) REVERT: A 961 LYS cc_start: 0.9274 (mttt) cc_final: 0.8980 (mppt) REVERT: A 1099 GLU cc_start: 0.8570 (pm20) cc_final: 0.8289 (pm20) REVERT: A 1208 ASN cc_start: 0.9177 (t0) cc_final: 0.8823 (t0) REVERT: A 1276 PHE cc_start: 0.8932 (t80) cc_final: 0.8643 (t80) REVERT: A 1337 ARG cc_start: 0.6884 (tpt90) cc_final: 0.6307 (tpt90) outliers start: 27 outliers final: 19 residues processed: 82 average time/residue: 0.1109 time to fit residues: 13.1841 Evaluate side-chains 81 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.089084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.065101 restraints weight = 42812.670| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.59 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11182 Z= 0.132 Angle : 0.568 9.777 15600 Z= 0.307 Chirality : 0.039 0.247 1820 Planarity : 0.003 0.039 1561 Dihedral : 19.539 151.837 2727 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.11 % Allowed : 20.51 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1008 helix: 0.67 (0.23), residues: 516 sheet: -0.33 (0.56), residues: 96 loop : -0.90 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.028 0.002 TYR A 988 PHE 0.023 0.002 PHE A 518 TRP 0.009 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11182) covalent geometry : angle 0.56831 / 0.31 (15600) hydrogen bonds : bond 0.04106 / 2.74 ( 447) hydrogen bonds : angle 4.33158 / 3.11 ( 1223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.4916 (p90) cc_final: 0.4314 (p90) REVERT: A 395 ARG cc_start: 0.8937 (mtm110) cc_final: 0.8677 (ttm-80) REVERT: A 601 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 961 LYS cc_start: 0.9278 (mttt) cc_final: 0.8989 (mppt) REVERT: A 1099 GLU cc_start: 0.8595 (pm20) cc_final: 0.8286 (pm20) REVERT: A 1208 ASN cc_start: 0.9180 (t0) cc_final: 0.8805 (t0) REVERT: A 1276 PHE cc_start: 0.8898 (t80) cc_final: 0.8653 (t80) REVERT: A 1337 ARG cc_start: 0.6766 (tpt90) cc_final: 0.6188 (tpt90) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.1134 time to fit residues: 12.6283 Evaluate side-chains 79 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1267 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.090734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067215 restraints weight = 46743.720| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.42 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11182 Z= 0.190 Angle : 0.608 9.571 15600 Z= 0.327 Chirality : 0.041 0.271 1820 Planarity : 0.004 0.037 1561 Dihedral : 19.554 152.834 2727 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.55 % Allowed : 20.07 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 1008 helix: 0.60 (0.23), residues: 516 sheet: -0.51 (0.56), residues: 96 loop : -1.02 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 635 TYR 0.034 0.002 TYR A 988 PHE 0.025 0.002 PHE A1258 TRP 0.010 0.001 TRP A1136 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (11182) covalent geometry : angle 0.60764 / 0.33 (15600) hydrogen bonds : bond 0.04836 / 3.24 ( 447) hydrogen bonds : angle 4.48062 / 3.19 ( 1223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.79 seconds wall clock time: 42 minutes 24.22 seconds (2544.22 seconds total)