Starting phenix.real_space_refine on Thu Jun 4 07:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.cif Found real_map, /net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22fn_68245/06_2026/22fn_68245.map" } resolution = 3.17 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= 0.006 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 64 5.49 5 S 21 5.16 5 C 6895 2.51 5 N 1887 2.21 5 O 2238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11105 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 484 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 21} Chain: "A" Number of atoms: 9772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9772 Classifications: {'peptide': 1202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 46, 'TRANS': 1155} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 849 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Time building chain proxies: 2.78, per 1000 atoms: 0.25 Number of scatterers: 11105 At special positions: 0 Unit cell: (102.9, 94.5, 131.25, 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 21 16.00 P 64 15.00 O 2238 8.00 N 1887 7.00 C 6895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 581.9 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 55.1% alpha, 10.1% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.732A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 68 Proline residue: A 52 - end of helix removed outlier: 3.761A pdb=" N LEU A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.598A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.591A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.847A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.222A pdb=" N PHE A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 180 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.949A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 4.459A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.599A pdb=" N ASN A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.752A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 343 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.995A pdb=" N HIS A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.779A pdb=" N SER A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.753A pdb=" N GLN A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 429 through 452 removed outlier: 3.915A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 484 removed outlier: 3.922A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 522 Proline residue: A 509 - end of helix removed outlier: 4.152A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.840A pdb=" N ILE A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.676A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 718 Proline residue: A 716 - end of helix Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.677A pdb=" N TRP A 765 " --> pdb=" O HIS A 761 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.912A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1024 removed outlier: 3.696A pdb=" N ASN A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 3.891A pdb=" N PHE A1101 " --> pdb=" O PHE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1189 Processing helix chain 'A' and resid 1192 through 1196 removed outlier: 3.927A pdb=" N GLY A1196 " --> pdb=" O PHE A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.812A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.823A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.687A pdb=" N PHE A1253 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1284 Processing helix chain 'A' and resid 1294 through 1307 removed outlier: 3.872A pdb=" N GLN A1303 " --> pdb=" O LEU A1299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.746A pdb=" N PHE A 531 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.746A pdb=" N PHE A 531 " --> pdb=" O TYR A 789 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.772A pdb=" N ARG A 267 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU A 272 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.725A pdb=" N ILE A 418 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 589 through 597 Processing sheet with id=AA6, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA7, first strand: chain 'A' and resid 926 through 931 removed outlier: 4.630A pdb=" N GLU A 928 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 919 " --> pdb=" O GLU A 928 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 990 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A1065 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 992 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1103 through 1107 Processing sheet with id=AA9, first strand: chain 'A' and resid 1144 through 1147 removed outlier: 3.635A pdb=" N GLU A1144 " --> pdb=" O ALA A1156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1226 through 1227 removed outlier: 3.732A pdb=" N TYR A1236 " --> pdb=" O ASN A1227 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.42 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: 2509 1.33 - 1.45: 2741 1.45 - 1.57: 6075 1.57 - 1.69: 126 1.69 - 1.81: 34 Bond restraints: 11485 Sorted by residual: bond pdb=" C4' DT C 35 " pdb=" C3' DT C 35 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C3' DT C 37 " pdb=" O3' DT C 37 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" C3' DA C 31 " pdb=" O3' DA C 31 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C3' DT C 32 " pdb=" C2' DT C 32 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.32e-01 bond pdb=" C4' DT C 39 " pdb=" O4' DT C 39 " ideal model delta sigma weight residual 1.450 1.432 0.018 2.00e-02 2.50e+03 7.70e-01 ... (remaining 11480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 15360 1.34 - 2.67: 366 2.67 - 4.01: 70 4.01 - 5.34: 17 5.34 - 6.68: 2 Bond angle restraints: 15815 Sorted by residual: angle pdb=" C VAL A1163 " pdb=" N ILE A1164 " pdb=" CA ILE A1164 " ideal model delta sigma weight residual 121.97 126.88 -4.91 1.80e+00 3.09e-01 7.44e+00 angle pdb=" CA TYR A 595 " pdb=" CB TYR A 595 " pdb=" CG TYR A 595 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.66e+00 angle pdb=" C THR A 934 " pdb=" N ILE A 935 " pdb=" CA ILE A 935 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.23e+00 angle pdb=" N ILE A 229 " pdb=" CA ILE A 229 " pdb=" CB ILE A 229 " ideal model delta sigma weight residual 112.33 109.68 2.65 1.19e+00 7.06e-01 4.97e+00 angle pdb=" C3' DA C 31 " pdb=" C2' DA C 31 " pdb=" C1' DA C 31 " ideal model delta sigma weight residual 101.60 104.77 -3.17 1.50e+00 4.44e-01 4.46e+00 ... (remaining 15810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6583 35.51 - 71.01: 218 71.01 - 106.52: 24 106.52 - 142.02: 1 142.02 - 177.53: 2 Dihedral angle restraints: 6828 sinusoidal: 3282 harmonic: 3546 Sorted by residual: dihedral pdb=" CA ASP A 163 " pdb=" C ASP A 163 " pdb=" N LYS A 164 " pdb=" CA LYS A 164 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DT C 37 " pdb=" C3' DT C 37 " pdb=" O3' DT C 37 " pdb=" P DA C 38 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG C 15 " pdb=" C3' DG C 15 " pdb=" O3' DG C 15 " pdb=" P DT C 16 " ideal model delta sinusoidal sigma weight residual 220.00 74.21 145.79 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 6825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1349 0.042 - 0.084: 317 0.084 - 0.126: 84 0.126 - 0.168: 8 0.168 - 0.210: 1 Chirality restraints: 1759 Sorted by residual: chirality pdb=" CB ILE A 905 " pdb=" CA ILE A 905 " pdb=" CG1 ILE A 905 " pdb=" CG2 ILE A 905 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 917 " pdb=" N ILE A 917 " pdb=" C ILE A 917 " pdb=" CB ILE A 917 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE A 907 " pdb=" N ILE A 907 " pdb=" C ILE A 907 " pdb=" CB ILE A 907 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1756 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT C 35 " -0.023 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" N1 DT C 35 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DT C 35 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT C 35 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DT C 35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT C 35 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT C 35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT C 35 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT C 35 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT C 35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 437 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLN A 437 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 437 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 438 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 34 " -0.021 2.00e-02 2.50e+03 1.06e-02 2.51e+00 pdb=" N1 DC C 34 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DC C 34 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DC C 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC C 34 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC C 34 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC C 34 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC C 34 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC C 34 " 0.005 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 6464 3.02 - 3.49: 11560 3.49 - 3.96: 18668 3.96 - 4.43: 22075 4.43 - 4.90: 32884 Nonbonded interactions: 91651 Sorted by model distance: nonbonded pdb=" O4' C B 15 " pdb=" C6 C B 15 " model vdw 2.555 2.672 nonbonded pdb=" O5' DT C 39 " pdb=" O4' DT C 39 " model vdw 2.565 2.432 nonbonded pdb=" O4' U B 18 " pdb=" C6 U B 18 " model vdw 2.590 2.672 nonbonded pdb=" N1 DG C 17 " pdb=" C4 DG C 17 " model vdw 2.596 2.672 nonbonded pdb=" N1 DG C 18 " pdb=" C4 DG C 18 " model vdw 2.596 2.672 ... (remaining 91646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.530 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: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.003 0.033 11485 Z= 0.136 Angle : 0.531 6.676 15815 Z= 0.291 Chirality : 0.039 0.210 1759 Planarity : 0.004 0.037 1806 Dihedral : 16.677 177.530 4532 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.86 (0.25), residues: 1194 helix: 1.23 (0.22), residues: 589 sheet: -1.15 (0.45), residues: 111 loop : 0.36 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.019 0.001 TYR A 595 PHE 0.015 0.001 PHE A 743 TRP 0.009 0.001 TRP A1258 HIS 0.012 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11485) covalent geometry : angle 0.53078 / 0.29 (15815) hydrogen bonds : bond 0.10737 / 6.20 ( 550) hydrogen bonds : angle 6.24890 / 4.21 ( 1543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.344 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: 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 28 LEU cc_start: 0.9354 (tp) cc_final: 0.9105 (pt) REVERT: A 65 CYS cc_start: 0.8559 (m) cc_final: 0.8318 (m) REVERT: A 445 HIS cc_start: 0.9563 (m90) cc_final: 0.9218 (m90) REVERT: A 477 LEU cc_start: 0.9788 (tp) cc_final: 0.9501 (mm) REVERT: A 518 ARG cc_start: 0.9331 (ttp-110) cc_final: 0.8848 (ttp-110) REVERT: A 642 ILE cc_start: 0.9488 (mm) cc_final: 0.9136 (tp) REVERT: A 893 ASN cc_start: 0.9006 (m-40) cc_final: 0.8801 (m-40) REVERT: A 1073 ILE cc_start: 0.8193 (mm) cc_final: 0.7580 (mt) REVERT: A 1192 VAL cc_start: 0.9268 (t) cc_final: 0.8689 (p) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1568 time to fit residues: 35.9500 Evaluate side-chains 90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS A 754 HIS A1105 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 ASN A1238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.063294 restraints weight = 39036.295| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.53 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11485 Z= 0.137 Angle : 0.579 10.853 15815 Z= 0.306 Chirality : 0.041 0.172 1759 Planarity : 0.004 0.041 1806 Dihedral : 17.645 176.967 2101 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 6.95 % Favored : 91.92 % 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: 1.21 (0.25), residues: 1194 helix: 1.68 (0.22), residues: 590 sheet: -1.05 (0.46), residues: 111 loop : 0.32 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.022 0.001 TYR A 746 PHE 0.019 0.001 PHE A 496 TRP 0.007 0.001 TRP A1258 HIS 0.010 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11485) covalent geometry : angle 0.57866 / 0.31 (15815) hydrogen bonds : bond 0.03890 / 2.32 ( 550) hydrogen bonds : angle 4.66815 / 3.09 ( 1543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.442 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 CYS cc_start: 0.8470 (m) cc_final: 0.8143 (m) REVERT: A 267 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8014 (tmm-80) REVERT: A 445 HIS cc_start: 0.9526 (m90) cc_final: 0.9149 (m-70) REVERT: A 477 LEU cc_start: 0.9808 (tp) cc_final: 0.9485 (mm) REVERT: A 506 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8824 (pp20) REVERT: A 507 MET cc_start: 0.9355 (mmt) cc_final: 0.8770 (tpp) REVERT: A 518 ARG cc_start: 0.9271 (ttp-110) cc_final: 0.8501 (ttp-110) REVERT: A 642 ILE cc_start: 0.9542 (mm) cc_final: 0.9082 (tp) REVERT: A 893 ASN cc_start: 0.9050 (m-40) cc_final: 0.8806 (m-40) REVERT: A 926 ILE cc_start: 0.9293 (tp) cc_final: 0.8872 (pt) REVERT: A 1073 ILE cc_start: 0.7907 (mm) cc_final: 0.7250 (mt) REVERT: A 1225 MET cc_start: 0.8832 (ppp) cc_final: 0.8150 (ppp) REVERT: A 1237 ILE cc_start: 0.9084 (tp) cc_final: 0.8821 (tp) outliers start: 12 outliers final: 4 residues processed: 107 average time/residue: 0.1426 time to fit residues: 20.4381 Evaluate side-chains 78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1069 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 111 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 HIS A1122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.085828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058965 restraints weight = 39571.305| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.51 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11485 Z= 0.237 Angle : 0.610 9.315 15815 Z= 0.324 Chirality : 0.042 0.149 1759 Planarity : 0.004 0.039 1806 Dihedral : 17.829 176.750 2101 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.69 % Allowed : 8.83 % Favored : 89.48 % 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: 1.16 (0.25), residues: 1194 helix: 1.66 (0.22), residues: 590 sheet: -1.16 (0.45), residues: 111 loop : 0.28 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 574 TYR 0.020 0.002 TYR A 595 PHE 0.021 0.002 PHE A 496 TRP 0.009 0.001 TRP A1258 HIS 0.012 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (11485) covalent geometry : angle 0.61007 / 0.32 (15815) hydrogen bonds : bond 0.03929 / 2.35 ( 550) hydrogen bonds : angle 4.58764 / 3.02 ( 1543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.410 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 CYS cc_start: 0.8544 (m) cc_final: 0.8309 (m) REVERT: A 239 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: A 267 ARG cc_start: 0.8604 (tmm-80) cc_final: 0.8075 (tmm-80) REVERT: A 433 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9202 (pm20) REVERT: A 445 HIS cc_start: 0.9561 (m90) cc_final: 0.9205 (m-70) REVERT: A 465 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 477 LEU cc_start: 0.9812 (tp) cc_final: 0.9472 (mm) REVERT: A 506 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8870 (pp20) REVERT: A 518 ARG cc_start: 0.9324 (ttp-110) cc_final: 0.8480 (ttp-110) REVERT: A 575 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: A 1073 ILE cc_start: 0.8341 (mm) cc_final: 0.7952 (mt) REVERT: A 1225 MET cc_start: 0.8820 (ppp) cc_final: 0.8544 (ppp) outliers start: 18 outliers final: 9 residues processed: 90 average time/residue: 0.1352 time to fit residues: 16.6159 Evaluate side-chains 82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1069 TYR Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 114 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A1044 GLN A1122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.088257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061924 restraints weight = 39317.989| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.51 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11485 Z= 0.119 Angle : 0.532 9.160 15815 Z= 0.283 Chirality : 0.039 0.157 1759 Planarity : 0.003 0.039 1806 Dihedral : 17.793 176.902 2101 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.41 % Allowed : 9.48 % Favored : 89.11 % 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: 1.30 (0.25), residues: 1194 helix: 1.82 (0.22), residues: 590 sheet: -1.11 (0.45), residues: 111 loop : 0.30 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1194 TYR 0.024 0.001 TYR A 746 PHE 0.020 0.001 PHE A 496 TRP 0.008 0.001 TRP A1136 HIS 0.008 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11485) covalent geometry : angle 0.53172 / 0.28 (15815) hydrogen bonds : bond 0.03375 / 2.00 ( 550) hydrogen bonds : angle 4.27997 / 2.83 ( 1543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.420 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9119 (tp30) cc_final: 0.8669 (pt0) REVERT: A 239 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: A 267 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8080 (tmm-80) REVERT: A 445 HIS cc_start: 0.9556 (m90) cc_final: 0.9187 (m-70) REVERT: A 465 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 477 LEU cc_start: 0.9805 (tp) cc_final: 0.9460 (mm) REVERT: A 506 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8928 (pp20) REVERT: A 518 ARG cc_start: 0.9301 (ttp-110) cc_final: 0.8494 (ttp-110) REVERT: A 893 ASN cc_start: 0.8981 (m-40) cc_final: 0.8764 (m-40) REVERT: A 967 LEU cc_start: 0.9417 (tp) cc_final: 0.9173 (tt) REVERT: A 1073 ILE cc_start: 0.8107 (mm) cc_final: 0.7627 (mt) REVERT: A 1225 MET cc_start: 0.8845 (ppp) cc_final: 0.8510 (ppp) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 0.1396 time to fit residues: 17.6257 Evaluate side-chains 79 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Chi-restraints excluded: chain A residue 1122 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 64 optimal weight: 0.0030 chunk 106 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.088118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061741 restraints weight = 39228.695| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.54 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11485 Z= 0.126 Angle : 0.539 9.945 15815 Z= 0.286 Chirality : 0.039 0.150 1759 Planarity : 0.003 0.045 1806 Dihedral : 17.776 176.642 2101 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.41 % Allowed : 10.61 % Favored : 87.98 % 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: 1.28 (0.25), residues: 1194 helix: 1.82 (0.22), residues: 590 sheet: -1.14 (0.44), residues: 113 loop : 0.28 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 411 TYR 0.015 0.001 TYR A 595 PHE 0.020 0.001 PHE A 496 TRP 0.007 0.001 TRP A1258 HIS 0.007 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11485) covalent geometry : angle 0.53871 / 0.29 (15815) hydrogen bonds : bond 0.03275 / 1.94 ( 550) hydrogen bonds : angle 4.22380 / 2.77 ( 1543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.426 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9131 (tp30) cc_final: 0.8676 (pt0) REVERT: A 267 ARG cc_start: 0.8645 (tmm-80) cc_final: 0.8156 (tmm-80) REVERT: A 445 HIS cc_start: 0.9547 (m90) cc_final: 0.9184 (m-70) REVERT: A 465 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8664 (mm-30) REVERT: A 506 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8879 (pp20) REVERT: A 507 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8428 (mmp) REVERT: A 518 ARG cc_start: 0.9278 (ttp-110) cc_final: 0.8487 (ttp-110) REVERT: A 893 ASN cc_start: 0.9001 (m-40) cc_final: 0.8774 (m-40) REVERT: A 967 LEU cc_start: 0.9418 (tp) cc_final: 0.9157 (tt) REVERT: A 1073 ILE cc_start: 0.8146 (mm) cc_final: 0.7692 (mt) REVERT: A 1225 MET cc_start: 0.8806 (ppp) cc_final: 0.8418 (ppp) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.1238 time to fit residues: 15.0314 Evaluate side-chains 83 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Chi-restraints excluded: chain A residue 1193 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.087598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061210 restraints weight = 39168.248| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.52 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11485 Z= 0.127 Angle : 0.533 9.266 15815 Z= 0.282 Chirality : 0.039 0.146 1759 Planarity : 0.003 0.031 1806 Dihedral : 17.740 176.549 2101 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 10.80 % Favored : 87.51 % 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: 1.37 (0.25), residues: 1194 helix: 1.92 (0.22), residues: 590 sheet: -1.07 (0.44), residues: 113 loop : 0.26 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.027 0.001 TYR A 746 PHE 0.020 0.001 PHE A 496 TRP 0.009 0.001 TRP A1136 HIS 0.007 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11485) covalent geometry : angle 0.53260 / 0.28 (15815) hydrogen bonds : bond 0.03203 / 1.90 ( 550) hydrogen bonds : angle 4.15331 / 2.73 ( 1543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.377 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9149 (tp30) cc_final: 0.8713 (pt0) REVERT: A 267 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8154 (tmm-80) REVERT: A 445 HIS cc_start: 0.9571 (m90) cc_final: 0.9196 (m-70) REVERT: A 465 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8654 (mm-30) REVERT: A 477 LEU cc_start: 0.9782 (tp) cc_final: 0.9486 (mm) REVERT: A 506 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8950 (pp20) REVERT: A 507 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8478 (mmp) REVERT: A 518 ARG cc_start: 0.9267 (ttp-110) cc_final: 0.8460 (ttp-110) REVERT: A 893 ASN cc_start: 0.9035 (m-40) cc_final: 0.8800 (m-40) REVERT: A 967 LEU cc_start: 0.9417 (tp) cc_final: 0.9162 (tt) REVERT: A 1073 ILE cc_start: 0.8227 (mm) cc_final: 0.7848 (mt) REVERT: A 1225 MET cc_start: 0.8754 (ppp) cc_final: 0.8431 (ppp) REVERT: A 1260 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7672 (mmm) outliers start: 18 outliers final: 10 residues processed: 86 average time/residue: 0.1271 time to fit residues: 15.4498 Evaluate side-chains 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Chi-restraints excluded: chain A residue 1260 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.088601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062220 restraints weight = 39216.873| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.52 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11485 Z= 0.114 Angle : 0.524 10.841 15815 Z= 0.275 Chirality : 0.039 0.146 1759 Planarity : 0.003 0.039 1806 Dihedral : 17.711 176.411 2101 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.22 % Allowed : 12.58 % Favored : 86.20 % 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: 1.42 (0.25), residues: 1194 helix: 1.98 (0.22), residues: 589 sheet: -1.01 (0.45), residues: 113 loop : 0.26 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.014 0.001 TYR A 595 PHE 0.020 0.001 PHE A 496 TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11485) covalent geometry : angle 0.52368 / 0.27 (15815) hydrogen bonds : bond 0.03115 / 1.84 ( 550) hydrogen bonds : angle 4.08511 / 2.69 ( 1543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.9143 (tp30) cc_final: 0.8685 (pt0) REVERT: A 267 ARG cc_start: 0.8709 (tmm-80) cc_final: 0.8160 (tmm-80) REVERT: A 445 HIS cc_start: 0.9554 (m90) cc_final: 0.9199 (m-70) REVERT: A 465 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8724 (mm-30) REVERT: A 477 LEU cc_start: 0.9763 (tp) cc_final: 0.9466 (mm) REVERT: A 506 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9003 (pp20) REVERT: A 507 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8418 (mmp) REVERT: A 518 ARG cc_start: 0.9203 (ttp-110) cc_final: 0.8378 (ttp-110) REVERT: A 893 ASN cc_start: 0.9044 (m-40) cc_final: 0.8817 (m-40) REVERT: A 967 LEU cc_start: 0.9394 (tp) cc_final: 0.9129 (tt) REVERT: A 1025 CYS cc_start: 0.8875 (t) cc_final: 0.8058 (p) REVERT: A 1073 ILE cc_start: 0.8195 (mm) cc_final: 0.7773 (mt) REVERT: A 1225 MET cc_start: 0.8703 (ppp) cc_final: 0.8409 (ppp) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.1302 time to fit residues: 16.0978 Evaluate side-chains 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 84 optimal weight: 0.2980 chunk 116 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.088060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061697 restraints weight = 38839.298| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 4.53 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11485 Z= 0.114 Angle : 0.526 9.850 15815 Z= 0.277 Chirality : 0.039 0.139 1759 Planarity : 0.003 0.037 1806 Dihedral : 17.680 176.270 2101 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.60 % Allowed : 12.21 % Favored : 86.20 % 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: 1.46 (0.25), residues: 1194 helix: 2.02 (0.23), residues: 589 sheet: -1.01 (0.44), residues: 113 loop : 0.26 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.029 0.001 TYR A 746 PHE 0.020 0.001 PHE A 496 TRP 0.006 0.001 TRP A1258 HIS 0.005 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (11485) covalent geometry : angle 0.52594 / 0.28 (15815) hydrogen bonds : bond 0.03080 / 1.82 ( 550) hydrogen bonds : angle 4.06007 / 2.67 ( 1543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.498 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9112 (m-30) cc_final: 0.8887 (p0) REVERT: A 123 LYS cc_start: 0.9536 (ttmt) cc_final: 0.9267 (mtmm) REVERT: A 174 GLU cc_start: 0.9156 (tp30) cc_final: 0.8703 (pt0) REVERT: A 267 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8132 (tmm-80) REVERT: A 445 HIS cc_start: 0.9557 (m90) cc_final: 0.9196 (m-70) REVERT: A 465 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8703 (mm-30) REVERT: A 477 LEU cc_start: 0.9760 (tp) cc_final: 0.9455 (mm) REVERT: A 518 ARG cc_start: 0.9188 (ttp-110) cc_final: 0.8350 (ttp-110) REVERT: A 893 ASN cc_start: 0.9070 (m-40) cc_final: 0.8836 (m-40) REVERT: A 967 LEU cc_start: 0.9403 (tp) cc_final: 0.9133 (tt) REVERT: A 1025 CYS cc_start: 0.8855 (t) cc_final: 0.8061 (p) REVERT: A 1073 ILE cc_start: 0.8224 (mm) cc_final: 0.7826 (mt) REVERT: A 1225 MET cc_start: 0.8689 (ppp) cc_final: 0.8422 (ppp) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.1297 time to fit residues: 15.6421 Evaluate side-chains 81 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059585 restraints weight = 38709.027| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.50 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11485 Z= 0.127 Angle : 0.557 9.482 15815 Z= 0.292 Chirality : 0.039 0.182 1759 Planarity : 0.003 0.035 1806 Dihedral : 17.655 176.185 2101 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.41 % Allowed : 12.49 % Favored : 86.10 % 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: 1.44 (0.25), residues: 1194 helix: 2.02 (0.22), residues: 589 sheet: -1.02 (0.44), residues: 113 loop : 0.24 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.015 0.001 TYR A 595 PHE 0.022 0.001 PHE A 496 TRP 0.007 0.001 TRP A1258 HIS 0.005 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11485) covalent geometry : angle 0.55676 / 0.29 (15815) hydrogen bonds : bond 0.03132 / 1.85 ( 550) hydrogen bonds : angle 4.08684 / 2.68 ( 1543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.436 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9258 (mtmm) REVERT: A 174 GLU cc_start: 0.9145 (tp30) cc_final: 0.8727 (pt0) REVERT: A 267 ARG cc_start: 0.8713 (tmm-80) cc_final: 0.8145 (tmm-80) REVERT: A 445 HIS cc_start: 0.9572 (m90) cc_final: 0.9193 (m-70) REVERT: A 465 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 477 LEU cc_start: 0.9763 (tp) cc_final: 0.9496 (mm) REVERT: A 499 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8410 (ttp-110) REVERT: A 518 ARG cc_start: 0.9186 (ttp-110) cc_final: 0.8342 (ttp-110) REVERT: A 893 ASN cc_start: 0.9057 (m-40) cc_final: 0.8817 (m-40) REVERT: A 967 LEU cc_start: 0.9397 (tp) cc_final: 0.9120 (tt) REVERT: A 1018 MET cc_start: 0.8662 (mtp) cc_final: 0.8118 (ttm) REVERT: A 1025 CYS cc_start: 0.8775 (t) cc_final: 0.8064 (p) REVERT: A 1073 ILE cc_start: 0.8292 (mm) cc_final: 0.7959 (mt) REVERT: A 1225 MET cc_start: 0.8660 (ppp) cc_final: 0.8383 (ppp) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1266 time to fit residues: 14.8805 Evaluate side-chains 84 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 17 optimal weight: 0.0010 chunk 107 optimal weight: 0.0770 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.088603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062204 restraints weight = 38909.715| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.54 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11485 Z= 0.112 Angle : 0.546 9.450 15815 Z= 0.287 Chirality : 0.039 0.165 1759 Planarity : 0.003 0.030 1806 Dihedral : 17.598 176.289 2101 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.22 % Allowed : 12.77 % Favored : 86.01 % 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: 1.47 (0.25), residues: 1194 helix: 2.04 (0.23), residues: 588 sheet: -0.95 (0.45), residues: 113 loop : 0.26 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 341 TYR 0.028 0.001 TYR A 746 PHE 0.024 0.001 PHE A 496 TRP 0.005 0.001 TRP A1136 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11485) covalent geometry : angle 0.54638 / 0.29 (15815) hydrogen bonds : bond 0.03076 / 1.82 ( 550) hydrogen bonds : angle 4.04018 / 2.66 ( 1543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.419 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9094 (m-30) cc_final: 0.8861 (p0) REVERT: A 123 LYS cc_start: 0.9522 (ttmt) cc_final: 0.9269 (mtmm) REVERT: A 174 GLU cc_start: 0.9154 (tp30) cc_final: 0.8693 (pt0) REVERT: A 267 ARG cc_start: 0.8755 (tmm-80) cc_final: 0.8275 (tmm-80) REVERT: A 445 HIS cc_start: 0.9561 (m90) cc_final: 0.9188 (m-70) REVERT: A 465 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8735 (mm-30) REVERT: A 477 LEU cc_start: 0.9754 (tp) cc_final: 0.9494 (mm) REVERT: A 499 ARG cc_start: 0.8735 (ttp-110) cc_final: 0.8518 (ttp-110) REVERT: A 518 ARG cc_start: 0.9168 (ttp-110) cc_final: 0.8310 (ttp-110) REVERT: A 893 ASN cc_start: 0.9079 (m-40) cc_final: 0.8839 (m-40) REVERT: A 926 ILE cc_start: 0.9212 (tp) cc_final: 0.8925 (pt) REVERT: A 967 LEU cc_start: 0.9369 (tp) cc_final: 0.9090 (tt) REVERT: A 1025 CYS cc_start: 0.8786 (t) cc_final: 0.8043 (p) REVERT: A 1073 ILE cc_start: 0.8305 (mm) cc_final: 0.7951 (mt) REVERT: A 1225 MET cc_start: 0.8629 (ppp) cc_final: 0.8384 (ppp) outliers start: 13 outliers final: 11 residues processed: 89 average time/residue: 0.1196 time to fit residues: 14.9915 Evaluate side-chains 86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 905 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1069 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN A1044 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.085240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058301 restraints weight = 39893.931| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.54 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11485 Z= 0.236 Angle : 0.621 9.482 15815 Z= 0.328 Chirality : 0.042 0.173 1759 Planarity : 0.003 0.029 1806 Dihedral : 17.779 175.740 2101 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.22 % Allowed : 13.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1194 helix: 1.91 (0.22), residues: 589 sheet: -1.17 (0.43), residues: 123 loop : 0.24 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.023 0.002 TYR A 595 PHE 0.025 0.002 PHE A 496 TRP 0.010 0.001 TRP A1258 HIS 0.008 0.001 HIS A1280 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (11485) covalent geometry : angle 0.62124 / 0.33 (15815) hydrogen bonds : bond 0.03605 / 2.15 ( 550) hydrogen bonds : angle 4.31378 / 2.85 ( 1543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.03 seconds wall clock time: 44 minutes 34.89 seconds (2674.89 seconds total)