Starting phenix.real_space_refine on Thu Jul 2 23:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t77_41086/07_2026/8t77_41086.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t77_41086/07_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_41086/07_2026/8t77_41086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2026/8t77_41086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_2026/8t77_41086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t77_41086/07_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-dev-6108/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: 2.64, per 1000 atoms: 0.25 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: 0.89 Conformation dependent library (CDL) restraints added in 262.8 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: 1.13 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: 2.22 Time building geometry restraints manager: 1.20 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: 15332 3.20 - 6.40: 230 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' 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 angle pdb=" N1 C B 18 " pdb=" C2 C B 18 " pdb=" O2 C B 18 " ideal model delta sigma weight residual 118.90 122.14 -3.24 6.00e-01 2.78e+00 2.92e+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: 1583 0.078 - 0.155: 214 0.155 - 0.233: 15 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- 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= 0.299 Angle : 1.004 16.010 15600 Z= 0.633 Chirality : 0.055 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 0.00473 / 0.30 (11182) covalent geometry : angle 1.00428 / 0.63 (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 : 0.381 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: 0.1113 time to fit residues: 13.8395 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 : 0.384 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN 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 = 0.4061 r_free = 0.4061 target = 0.091219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.067458 restraints weight = 42630.207| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.57 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1587 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= 0.260 Angle : 0.718 9.908 15600 Z= 0.392 Chirality : 0.044 0.252 1820 Planarity : 0.005 0.039 1561 Dihedral : 20.013 156.670 2729 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -0.79 (0.25), residues: 1008 helix: -0.19 (0.22), residues: 517 sheet: -0.74 (0.52), residues: 101 loop : -0.72 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 654 TYR 0.025 0.002 TYR A 362 PHE 0.014 0.002 PHE A 196 TRP 0.025 0.003 TRP A 18 HIS 0.006 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.26 (11182) covalent geometry : angle 0.71787 / 0.39 (15600) hydrogen bonds : bond 0.06208 / 4.15 ( 447) hydrogen bonds : angle 5.20952 / 3.70 ( 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 98 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 MET cc_start: 0.5021 (ttm) cc_final: 0.4767 (ttm) REVERT: A 397 ASP cc_start: 0.8053 (t0) cc_final: 0.7781 (t0) REVERT: A 738 LEU cc_start: 0.8455 (mp) cc_final: 0.8251 (tt) REVERT: A 1337 ARG cc_start: 0.7024 (tpt90) cc_final: 0.6810 (tpt90) outliers start: 27 outliers final: 17 residues processed: 90 average time/residue: 0.1008 time to fit residues: 13.5931 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 : 0.367 ------------------------------------------------------------------------------- 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 657 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 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: 9.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4089 r_free = 0.4089 target = 0.092643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.068701 restraints weight = 42194.523| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.62 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11182 Z= 0.133 Angle : 0.567 9.749 15600 Z= 0.315 Chirality : 0.039 0.199 1820 Planarity : 0.004 0.034 1561 Dihedral : 19.963 154.622 2727 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.05 % 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: -0.41 (0.26), residues: 1008 helix: 0.19 (0.23), residues: 516 sheet: -0.49 (0.53), residues: 101 loop : -0.67 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.024 0.002 TYR A 988 PHE 0.018 0.002 PHE A 966 TRP 0.014 0.002 TRP A 18 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (11182) covalent geometry : angle 0.56672 / 0.31 (15600) hydrogen bonds : bond 0.04737 / 3.17 ( 447) hydrogen bonds : angle 4.86025 / 3.47 ( 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 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8156 (t0) cc_final: 0.7892 (t0) REVERT: A 961 LYS cc_start: 0.9270 (mttt) cc_final: 0.9002 (mppt) REVERT: A 1337 ARG cc_start: 0.6900 (tpt90) cc_final: 0.6621 (tpt90) outliers start: 27 outliers final: 12 residues processed: 92 average time/residue: 0.1031 time to fit residues: 13.9408 Evaluate side-chains 80 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 466 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: 4.9990 chunk 10 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 GLN A 754 HIS ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.089977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065812 restraints weight = 43456.195| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.48 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 11182 Z= 0.202 Angle : 0.607 8.789 15600 Z= 0.336 Chirality : 0.040 0.230 1820 Planarity : 0.004 0.034 1561 Dihedral : 19.856 155.459 2727 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.66 % Allowed : 17.85 % 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: -0.40 (0.25), residues: 1008 helix: 0.36 (0.23), residues: 517 sheet: -0.58 (0.53), residues: 96 loop : -0.90 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 654 TYR 0.019 0.002 TYR A 450 PHE 0.019 0.002 PHE A 693 TRP 0.011 0.002 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (11182) covalent geometry : angle 0.60703 / 0.34 (15600) hydrogen bonds : bond 0.05412 / 3.63 ( 447) hydrogen bonds : angle 4.73345 / 3.37 ( 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 105 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 LEU cc_start: 0.9043 (tp) cc_final: 0.8834 (tt) REVERT: A 397 ASP cc_start: 0.8301 (t0) cc_final: 0.8039 (t0) REVERT: A 650 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: A 961 LYS cc_start: 0.9276 (mttt) cc_final: 0.9000 (mppt) REVERT: A 1099 GLU cc_start: 0.8583 (pm20) cc_final: 0.8237 (pm20) REVERT: A 1337 ARG cc_start: 0.6943 (tpt90) cc_final: 0.6538 (tpt90) outliers start: 33 outliers final: 24 residues processed: 97 average time/residue: 0.1033 time to fit residues: 14.6416 Evaluate side-chains 90 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 650 GLN 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 1089 MET 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 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 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 86 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.091287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.067527 restraints weight = 41639.474| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.39 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11182 Z= 0.129 Angle : 0.548 9.266 15600 Z= 0.302 Chirality : 0.039 0.354 1820 Planarity : 0.003 0.043 1561 Dihedral : 19.835 153.886 2727 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.22 % Allowed : 17.96 % 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: -0.22 (0.26), residues: 1008 helix: 0.46 (0.23), residues: 517 sheet: -0.36 (0.54), residues: 96 loop : -0.78 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.026 0.002 TYR A 988 PHE 0.016 0.001 PHE A 966 TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (11182) covalent geometry : angle 0.54813 / 0.30 (15600) hydrogen bonds : bond 0.04478 / 2.96 ( 447) hydrogen bonds : angle 4.57982 / 3.28 ( 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 101 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.314 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: A 397 ASP cc_start: 0.8324 (t0) cc_final: 0.8060 (t0) REVERT: A 650 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (pp30) REVERT: A 961 LYS cc_start: 0.9272 (mttt) cc_final: 0.8992 (mppt) REVERT: A 1099 GLU cc_start: 0.8539 (pm20) cc_final: 0.8240 (pm20) REVERT: A 1108 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 1326 TYR cc_start: 0.7375 (t80) cc_final: 0.7174 (t80) REVERT: A 1337 ARG cc_start: 0.6794 (tpt90) cc_final: 0.6367 (tpt90) outliers start: 29 outliers final: 17 residues processed: 92 average time/residue: 0.1055 time to fit residues: 14.0600 Evaluate side-chains 83 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL 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 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 742 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 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 650 GLN ** A1261 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 = 0.4069 r_free = 0.4069 target = 0.090811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.066973 restraints weight = 42284.019| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.43 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11182 Z= 0.136 Angle : 0.550 9.134 15600 Z= 0.300 Chirality : 0.038 0.196 1820 Planarity : 0.003 0.045 1561 Dihedral : 19.731 153.375 2727 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.22 % Allowed : 18.63 % 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: -0.20 (0.26), residues: 1008 helix: 0.47 (0.23), residues: 518 sheet: -0.31 (0.54), residues: 96 loop : -0.78 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.020 0.002 TYR A 988 PHE 0.015 0.002 PHE A 966 TRP 0.008 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (11182) covalent geometry : angle 0.54963 / 0.30 (15600) hydrogen bonds : bond 0.04401 / 2.93 ( 447) hydrogen bonds : angle 4.45198 / 3.20 ( 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 99 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.388 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: A 397 ASP cc_start: 0.8379 (t0) cc_final: 0.8118 (t0) REVERT: A 961 LYS cc_start: 0.9266 (mttt) cc_final: 0.8983 (mppt) REVERT: A 1099 GLU cc_start: 0.8543 (pm20) cc_final: 0.8260 (pm20) REVERT: A 1108 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 1208 ASN cc_start: 0.9198 (t0) cc_final: 0.8979 (t0) REVERT: A 1337 ARG cc_start: 0.6858 (tpt90) cc_final: 0.6403 (tpt90) outliers start: 29 outliers final: 23 residues processed: 90 average time/residue: 0.1096 time to fit residues: 14.2458 Evaluate side-chains 91 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 742 LYS 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 1108 GLU Chi-restraints excluded: chain A residue 1142 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** 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 = 0.4066 r_free = 0.4066 target = 0.090642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066820 restraints weight = 41781.773| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.39 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11182 Z= 0.134 Angle : 0.542 10.372 15600 Z= 0.296 Chirality : 0.038 0.313 1820 Planarity : 0.003 0.043 1561 Dihedral : 19.669 153.006 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.55 % Allowed : 18.96 % Favored : 77.49 % 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: 0.55 (0.23), residues: 517 sheet: -0.26 (0.55), residues: 96 loop : -0.81 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.026 0.002 TYR A 988 PHE 0.047 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 0.00274 / 0.13 (11182) covalent geometry : angle 0.54221 / 0.30 (15600) hydrogen bonds : bond 0.04257 / 2.85 ( 447) hydrogen bonds : angle 4.40380 / 3.16 ( 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 96 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8374 (t0) cc_final: 0.8147 (t0) REVERT: A 961 LYS cc_start: 0.9263 (mttt) cc_final: 0.8976 (mppt) REVERT: A 1099 GLU cc_start: 0.8539 (pm20) cc_final: 0.8267 (pm20) REVERT: A 1108 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 1123 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7614 (mmtm) REVERT: A 1208 ASN cc_start: 0.9187 (t0) cc_final: 0.8931 (t0) REVERT: A 1276 PHE cc_start: 0.8865 (t80) cc_final: 0.8606 (t80) REVERT: A 1337 ARG cc_start: 0.6812 (tpt90) cc_final: 0.6304 (tpt90) outliers start: 32 outliers final: 22 residues processed: 87 average time/residue: 0.1131 time to fit residues: 14.2178 Evaluate side-chains 87 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 466 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER 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 1108 GLU Chi-restraints excluded: chain A residue 1123 LYS Chi-restraints excluded: chain A residue 1142 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** 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 = 0.4001 r_free = 0.4001 target = 0.087441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063547 restraints weight = 42520.817| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 4.48 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11182 Z= 0.200 Angle : 0.591 9.420 15600 Z= 0.323 Chirality : 0.040 0.267 1820 Planarity : 0.004 0.039 1561 Dihedral : 19.683 154.960 2727 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.55 % Allowed : 19.62 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 1008 helix: 0.51 (0.23), residues: 519 sheet: -0.43 (0.55), residues: 96 loop : -0.99 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 654 TYR 0.024 0.002 TYR A 450 PHE 0.034 0.002 PHE A1258 TRP 0.009 0.002 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (11182) covalent geometry : angle 0.59114 / 0.32 (15600) hydrogen bonds : bond 0.05062 / 3.37 ( 447) hydrogen bonds : angle 4.55486 / 3.24 ( 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: 32 poor density : 62 time to evaluate : 0.369 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: A 130 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (pp20) REVERT: A 397 ASP cc_start: 0.8485 (t0) cc_final: 0.8236 (t0) REVERT: A 492 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9303 (pp) REVERT: A 650 GLN cc_start: 0.8372 (pt0) cc_final: 0.7722 (pt0) REVERT: A 961 LYS cc_start: 0.9294 (mttt) cc_final: 0.9001 (mppt) REVERT: A 1099 GLU cc_start: 0.8623 (pm20) cc_final: 0.8314 (pm20) REVERT: A 1108 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 1123 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7899 (mmtt) REVERT: A 1208 ASN cc_start: 0.9170 (t0) cc_final: 0.8811 (t0) REVERT: A 1337 ARG cc_start: 0.6854 (tpt90) cc_final: 0.6255 (tpt90) outliers start: 32 outliers final: 22 residues processed: 83 average time/residue: 0.1097 time to fit residues: 13.2682 Evaluate side-chains 87 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 130 GLU 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 492 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 512 SER 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 1108 GLU Chi-restraints excluded: chain A residue 1123 LYS Chi-restraints excluded: chain A residue 1142 SER 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 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP 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: 3.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.091095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.067571 restraints weight = 46175.675| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 4.41 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11182 Z= 0.168 Angle : 0.565 10.915 15600 Z= 0.310 Chirality : 0.039 0.294 1820 Planarity : 0.004 0.039 1561 Dihedral : 19.712 154.416 2727 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.10 % Allowed : 19.96 % Favored : 76.94 % 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: -0.29 (0.26), residues: 1008 helix: 0.52 (0.23), residues: 519 sheet: -0.41 (0.55), residues: 96 loop : -0.99 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.041 0.002 TYR A 988 PHE 0.041 0.002 PHE A1258 TRP 0.010 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (11182) covalent geometry : angle 0.56478 / 0.31 (15600) hydrogen bonds : bond 0.04419 / 2.96 ( 447) hydrogen bonds : angle 4.47340 / 3.19 ( 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 95 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.354 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: A 196 PHE cc_start: 0.4856 (p90) cc_final: 0.4307 (p90) REVERT: A 395 ARG cc_start: 0.9022 (mtm110) cc_final: 0.8724 (ttm-80) REVERT: A 492 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9290 (pp) REVERT: A 650 GLN cc_start: 0.8393 (pt0) cc_final: 0.7770 (pt0) REVERT: A 961 LYS cc_start: 0.9283 (mttt) cc_final: 0.8991 (mppt) REVERT: A 1099 GLU cc_start: 0.8583 (pm20) cc_final: 0.8296 (pm20) REVERT: A 1108 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: A 1123 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (mmtt) REVERT: A 1208 ASN cc_start: 0.9164 (t0) cc_final: 0.8778 (t0) outliers start: 28 outliers final: 21 residues processed: 86 average time/residue: 0.1081 time to fit residues: 13.4423 Evaluate side-chains 87 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 492 ILE Chi-restraints excluded: chain A residue 512 SER 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 1108 GLU Chi-restraints excluded: chain A residue 1123 LYS Chi-restraints excluded: chain A residue 1142 SER 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 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** 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 = 0.4046 r_free = 0.4046 target = 0.091196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067202 restraints weight = 46128.895| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.52 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11182 Z= 0.154 Angle : 0.577 12.000 15600 Z= 0.314 Chirality : 0.039 0.226 1820 Planarity : 0.004 0.039 1561 Dihedral : 19.677 153.711 2727 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.66 % Allowed : 20.62 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.26), residues: 1008 helix: 0.57 (0.23), residues: 519 sheet: -0.44 (0.55), residues: 96 loop : -0.99 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1337 TYR 0.022 0.002 TYR A 450 PHE 0.038 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 0.00322 / 0.15 (11182) covalent geometry : angle 0.57653 / 0.31 (15600) hydrogen bonds : bond 0.04383 / 2.91 ( 447) hydrogen bonds : angle 4.44750 / 3.18 ( 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 87 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.361 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: A 196 PHE cc_start: 0.4772 (p90) cc_final: 0.4234 (p90) REVERT: A 395 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8730 (ttm-80) REVERT: A 492 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9262 (pp) REVERT: A 650 GLN cc_start: 0.8380 (pt0) cc_final: 0.7761 (pt0) REVERT: A 961 LYS cc_start: 0.9280 (mttt) cc_final: 0.8986 (mppt) REVERT: A 1099 GLU cc_start: 0.8594 (pm20) cc_final: 0.8290 (pm20) REVERT: A 1108 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 1123 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7889 (mmtt) REVERT: A 1208 ASN cc_start: 0.9155 (t0) cc_final: 0.8755 (t0) outliers start: 24 outliers final: 21 residues processed: 81 average time/residue: 0.1034 time to fit residues: 11.9949 Evaluate side-chains 86 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 492 ILE Chi-restraints excluded: chain A residue 512 SER 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 1108 GLU Chi-restraints excluded: chain A residue 1123 LYS Chi-restraints excluded: chain A residue 1142 SER 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 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL 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: 3.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.092202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.068741 restraints weight = 46222.723| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.45 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11182 Z= 0.123 Angle : 0.548 10.606 15600 Z= 0.298 Chirality : 0.038 0.289 1820 Planarity : 0.003 0.039 1561 Dihedral : 19.621 152.340 2727 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.99 % Allowed : 20.95 % Favored : 76.05 % 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: -0.19 (0.26), residues: 1008 helix: 0.62 (0.23), residues: 520 sheet: -0.21 (0.61), residues: 81 loop : -1.01 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1337 TYR 0.036 0.002 TYR A 988 PHE 0.039 0.002 PHE A1258 TRP 0.009 0.001 TRP A1136 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11182) covalent geometry : angle 0.54797 / 0.30 (15600) hydrogen bonds : bond 0.03995 / 2.66 ( 447) hydrogen bonds : angle 4.34227 / 3.11 ( 1223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.62 seconds wall clock time: 45 minutes 9.37 seconds (2709.37 seconds total)