Starting phenix.real_space_refine on Wed Aug 5 13:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6h_62127/08_2026/9k6h_62127.cif" } resolution = 3.0 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= 0.042 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 1 6.06 5 P 57 5.49 5 S 39 5.16 5 C 6041 2.51 5 N 1651 2.21 5 O 1861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8525 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 984} Chain: "B" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 404 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MN': 1, ' ZN': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7311 SG CYS A1130 51.993 76.145 14.243 1.00 60.51 S ATOM 7346 SG CYS A1134 52.108 75.587 10.513 1.00 72.68 S ATOM 7452 SG CYS A1147 49.786 73.386 12.649 1.00 52.84 S Time building chain proxies: 2.16, per 1000 atoms: 0.22 Number of scatterers: 9651 At special positions: 0 Unit cell: (86, 125, 114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 1 24.99 S 39 16.00 P 57 15.00 O 1861 8.00 N 1651 7.00 C 6041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 333.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1134 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1147 " Number of angles added : 3 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 65.6% alpha, 6.8% beta 16 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.915A pdb=" N LEU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 283 through 311 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.640A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.802A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.854A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.667A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.717A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.577A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 785 through 800 Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.944A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.774A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 3.774A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.946A pdb=" N ARG A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.725A pdb=" N LEU A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.637A pdb=" N ILE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.840A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1006 removed outlier: 4.206A pdb=" N MET A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.696A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.503A pdb=" N LYS A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1163 Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.653A pdb=" N THR A1207 " --> pdb=" O THR A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1238 Processing helix chain 'A' and resid 1239 through 1257 removed outlier: 5.688A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.668A pdb=" N ILE A 393 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 401 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.411A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.411A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 768 475 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.36 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: 2374 1.33 - 1.45: 2083 1.45 - 1.57: 5341 1.57 - 1.69: 109 1.69 - 1.81: 63 Bond restraints: 9970 Sorted by residual: bond pdb=" C1' DC B 15 " pdb=" N1 DC B 15 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.31e+00 bond pdb=" C1' DC B 20 " pdb=" N1 DC B 20 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.24e+00 bond pdb=" C3' DT C 30 " pdb=" C2' DT C 30 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.28e+00 bond pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.41e+00 bond pdb=" C1' DT C 27 " pdb=" N1 DT C 27 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.40e+00 ... (remaining 9965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13117 1.44 - 2.88: 472 2.88 - 4.32: 60 4.32 - 5.76: 20 5.76 - 7.20: 3 Bond angle restraints: 13672 Sorted by residual: angle pdb=" N3 DT C 23 " pdb=" C4 DT C 23 " pdb=" O4 DT C 23 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 30 " pdb=" C4 DT C 30 " pdb=" O4 DT C 30 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 27 " pdb=" C4 DT C 27 " pdb=" O4 DT C 27 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 28 " pdb=" C4 DT C 28 " pdb=" O4 DT C 28 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 13667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 5236 20.71 - 41.42: 600 41.42 - 62.13: 210 62.13 - 82.84: 18 82.84 - 103.55: 5 Dihedral angle restraints: 6069 sinusoidal: 3022 harmonic: 3047 Sorted by residual: dihedral pdb=" CA PHE A 605 " pdb=" C PHE A 605 " pdb=" N ASP A 606 " pdb=" CA ASP A 606 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" O4' U E 24 " pdb=" C1' U E 24 " pdb=" N1 U E 24 " pdb=" C2 U E 24 " ideal model delta sinusoidal sigma weight residual -160.00 -108.32 -51.68 1 1.50e+01 4.44e-03 1.62e+01 dihedral pdb=" CA TRP A1145 " pdb=" C TRP A1145 " pdb=" N ASP A1146 " pdb=" CA ASP A1146 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 977 0.034 - 0.068: 366 0.068 - 0.102: 128 0.102 - 0.136: 43 0.136 - 0.170: 7 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ILE A 407 " pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CB ILE A 407 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB ILE A 359 " pdb=" CA ILE A 359 " pdb=" CG1 ILE A 359 " pdb=" CG2 ILE A 359 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB THR A 882 " pdb=" CA THR A 882 " pdb=" OG1 THR A 882 " pdb=" CG2 THR A 882 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1518 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C ILE A 390 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 390 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 786 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 787 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 787 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 787 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 367 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.71e+00 pdb=" CG PHE A 367 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 367 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 367 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 367 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 367 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 367 " -0.002 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 19 2.64 - 3.20: 8590 3.20 - 3.77: 16300 3.77 - 4.33: 22127 4.33 - 4.90: 35415 Nonbonded interactions: 82451 Sorted by model distance: nonbonded pdb=" O ASN A1066 " pdb=" OD1 ASN A1066 " model vdw 2.069 3.040 nonbonded pdb=" O ALA A 601 " pdb="MN MN A1303 " model vdw 2.129 2.320 nonbonded pdb=" OD2 ASP A 702 " pdb="MN MN A1303 " model vdw 2.171 2.320 nonbonded pdb=" O2B DTP A1301 " pdb="MN MN A1303 " model vdw 2.185 2.320 nonbonded pdb=" O1A DTP A1301 " pdb="MN MN A1303 " model vdw 2.191 2.320 ... (remaining 82446 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.004 0.059 9974 Z= 0.257 Angle : 0.632 7.204 13675 Z= 0.424 Chirality : 0.043 0.170 1521 Planarity : 0.004 0.041 1514 Dihedral : 18.726 103.550 4085 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 1.06 % Allowed : 23.33 % Favored : 75.61 % 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 (0.27), residues: 1026 helix: 1.54 (0.21), residues: 604 sheet: -1.21 (0.69), residues: 49 loop : 0.53 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.016 0.001 TYR A1112 PHE 0.029 0.002 PHE A 367 TRP 0.012 0.001 TRP A1011 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.26 ( 9970) covalent geometry : angle 0.63142 / 0.42 (13672) hydrogen bonds : bond 0.11098 / 7.02 ( 501) hydrogen bonds : angle 5.59797 / 4.19 ( 1456) metal coordination : bond 0.00543 / 0.24 ( 4) metal coordination : angle 1.83819 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.7547 (mttt) cc_final: 0.7274 (mtmm) REVERT: A 271 LYS cc_start: 0.7283 (tttt) cc_final: 0.6746 (tmmt) REVERT: A 474 ASP cc_start: 0.8164 (p0) cc_final: 0.7891 (p0) REVERT: A 654 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7681 (mmtt) REVERT: A 732 LYS cc_start: 0.8163 (tppp) cc_final: 0.7768 (mtpt) REVERT: A 744 THR cc_start: 0.8863 (m) cc_final: 0.8359 (p) REVERT: A 800 LYS cc_start: 0.8085 (pttt) cc_final: 0.7720 (ptmm) REVERT: A 1002 MET cc_start: 0.6500 (mmp) cc_final: 0.6273 (tpp) REVERT: A 1017 LYS cc_start: 0.7314 (tttt) cc_final: 0.6996 (ttmt) REVERT: A 1026 THR cc_start: 0.8154 (m) cc_final: 0.7738 (p) REVERT: A 1044 SER cc_start: 0.8647 (p) cc_final: 0.8414 (t) REVERT: A 1171 ASP cc_start: 0.7501 (t0) cc_final: 0.7285 (m-30) REVERT: A 1210 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7725 (mp10) REVERT: A 1264 THR cc_start: 0.8031 (m) cc_final: 0.7701 (p) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.6166 time to fit residues: 90.6766 Evaluate side-chains 126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.185549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.140492 restraints weight = 10151.915| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.55 r_work: 0.3320 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9974 Z= 0.165 Angle : 0.560 8.020 13675 Z= 0.305 Chirality : 0.041 0.141 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.799 106.386 1842 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Rotamer: Outliers : 3.39 % Allowed : 21.00 % Favored : 75.61 % 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: 1.64 (0.27), residues: 1026 helix: 1.76 (0.21), residues: 596 sheet: -0.98 (0.72), residues: 44 loop : 0.41 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.024 0.002 PHE A 605 TRP 0.012 0.001 TRP A1247 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9970) covalent geometry : angle 0.55977 / 0.30 (13672) hydrogen bonds : bond 0.04427 / 2.97 ( 501) hydrogen bonds : angle 4.56164 / 3.38 ( 1456) metal coordination : bond 0.00844 / 0.36 ( 4) metal coordination : angle 1.87681 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.366 Fit side-chains REVERT: A 251 LYS cc_start: 0.7590 (mttt) cc_final: 0.7354 (mttp) REVERT: A 271 LYS cc_start: 0.7356 (tttt) cc_final: 0.6809 (tmmt) REVERT: A 474 ASP cc_start: 0.8123 (p0) cc_final: 0.7889 (p0) REVERT: A 550 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8640 (mmm-85) REVERT: A 571 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7627 (mm-40) REVERT: A 732 LYS cc_start: 0.8152 (tppp) cc_final: 0.7770 (mtpt) REVERT: A 736 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7588 (mm110) REVERT: A 744 THR cc_start: 0.8913 (m) cc_final: 0.8540 (p) REVERT: A 800 LYS cc_start: 0.8199 (pttt) cc_final: 0.7791 (ptmm) REVERT: A 995 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7134 (mmm) REVERT: A 1002 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6407 (tpp) REVERT: A 1017 LYS cc_start: 0.7385 (tttt) cc_final: 0.7023 (ttmt) REVERT: A 1026 THR cc_start: 0.8185 (m) cc_final: 0.7788 (p) REVERT: A 1044 SER cc_start: 0.8635 (p) cc_final: 0.8380 (t) REVERT: A 1123 LYS cc_start: 0.7521 (mmtt) cc_final: 0.6772 (mtmp) REVERT: A 1171 ASP cc_start: 0.7582 (t0) cc_final: 0.7337 (m-30) REVERT: A 1210 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7849 (mp10) REVERT: A 1223 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (mtp) REVERT: A 1264 THR cc_start: 0.8014 (m) cc_final: 0.7707 (p) outliers start: 32 outliers final: 10 residues processed: 146 average time/residue: 0.5780 time to fit residues: 90.8051 Evaluate side-chains 131 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 563 GLN A 736 GLN A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139344 restraints weight = 10202.570| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.49 r_work: 0.3295 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9974 Z= 0.167 Angle : 0.550 8.780 13675 Z= 0.298 Chirality : 0.041 0.147 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.753 107.903 1837 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Rotamer: Outliers : 3.82 % Allowed : 20.47 % Favored : 75.72 % 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: 1.59 (0.27), residues: 1026 helix: 1.77 (0.21), residues: 599 sheet: -1.10 (0.72), residues: 44 loop : 0.31 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.026 0.002 PHE A 605 TRP 0.008 0.001 TRP A1158 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9970) covalent geometry : angle 0.54927 / 0.30 (13672) hydrogen bonds : bond 0.04120 / 2.77 ( 501) hydrogen bonds : angle 4.38173 / 3.23 ( 1456) metal coordination : bond 0.00823 / 0.34 ( 4) metal coordination : angle 1.73257 / 0.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.217 Fit side-chains REVERT: A 251 LYS cc_start: 0.7545 (mttt) cc_final: 0.7287 (mttp) REVERT: A 271 LYS cc_start: 0.7385 (tttt) cc_final: 0.6818 (tmmt) REVERT: A 474 ASP cc_start: 0.8137 (p0) cc_final: 0.7899 (p0) REVERT: A 523 ASP cc_start: 0.7573 (t0) cc_final: 0.7360 (t0) REVERT: A 571 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: A 732 LYS cc_start: 0.8160 (tppp) cc_final: 0.7683 (mtpt) REVERT: A 744 THR cc_start: 0.8973 (m) cc_final: 0.8657 (p) REVERT: A 754 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6919 (mpt) REVERT: A 800 LYS cc_start: 0.8143 (pttt) cc_final: 0.7709 (ptmm) REVERT: A 975 LYS cc_start: 0.7753 (mttt) cc_final: 0.7459 (pttm) REVERT: A 995 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7130 (mmm) REVERT: A 1002 MET cc_start: 0.6735 (mmp) cc_final: 0.6502 (tpp) REVERT: A 1017 LYS cc_start: 0.7352 (tttt) cc_final: 0.6955 (ttmt) REVERT: A 1026 THR cc_start: 0.8125 (m) cc_final: 0.7700 (p) REVERT: A 1044 SER cc_start: 0.8636 (p) cc_final: 0.8378 (t) REVERT: A 1086 TYR cc_start: 0.7348 (t80) cc_final: 0.7141 (t80) REVERT: A 1123 LYS cc_start: 0.7568 (mmtt) cc_final: 0.6808 (mtmp) REVERT: A 1155 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7721 (mttt) REVERT: A 1171 ASP cc_start: 0.7650 (t0) cc_final: 0.7389 (m-30) REVERT: A 1210 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7415 (mp-120) REVERT: A 1229 MET cc_start: 0.8776 (mmp) cc_final: 0.8546 (mmp) REVERT: A 1264 THR cc_start: 0.7997 (m) cc_final: 0.7699 (p) outliers start: 36 outliers final: 15 residues processed: 146 average time/residue: 0.5113 time to fit residues: 80.5067 Evaluate side-chains 129 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.183336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139019 restraints weight = 10190.534| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.49 r_work: 0.3297 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9974 Z= 0.161 Angle : 0.545 9.328 13675 Z= 0.293 Chirality : 0.041 0.147 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.702 107.664 1834 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 4.03 % Allowed : 20.47 % Favored : 75.50 % 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: 1.58 (0.27), residues: 1026 helix: 1.78 (0.21), residues: 599 sheet: -1.15 (0.72), residues: 44 loop : 0.27 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.025 0.002 PHE A 605 TRP 0.012 0.001 TRP A 899 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 9970) covalent geometry : angle 0.54428 / 0.29 (13672) hydrogen bonds : bond 0.03943 / 2.66 ( 501) hydrogen bonds : angle 4.28827 / 3.17 ( 1456) metal coordination : bond 0.00901 / 0.36 ( 4) metal coordination : angle 1.72726 / 0.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.7471 (mttt) cc_final: 0.7235 (mttp) REVERT: A 271 LYS cc_start: 0.7413 (tttt) cc_final: 0.6827 (tmmt) REVERT: A 474 ASP cc_start: 0.8133 (p0) cc_final: 0.7904 (p0) REVERT: A 571 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7680 (mm-40) REVERT: A 732 LYS cc_start: 0.8178 (tppp) cc_final: 0.7687 (mtpt) REVERT: A 744 THR cc_start: 0.8968 (m) cc_final: 0.8663 (p) REVERT: A 800 LYS cc_start: 0.8151 (pttt) cc_final: 0.7718 (ptmm) REVERT: A 908 MET cc_start: 0.7654 (ptm) cc_final: 0.7418 (ptm) REVERT: A 934 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7832 (tmtt) REVERT: A 975 LYS cc_start: 0.7747 (mttt) cc_final: 0.7467 (pttm) REVERT: A 995 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: A 1002 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6497 (tpp) REVERT: A 1026 THR cc_start: 0.8106 (m) cc_final: 0.7689 (p) REVERT: A 1044 SER cc_start: 0.8632 (p) cc_final: 0.8366 (t) REVERT: A 1155 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7648 (mtmt) REVERT: A 1171 ASP cc_start: 0.7608 (t0) cc_final: 0.7364 (m-30) REVERT: A 1210 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7516 (mp-120) REVERT: A 1264 THR cc_start: 0.8053 (m) cc_final: 0.7752 (p) outliers start: 38 outliers final: 12 residues processed: 144 average time/residue: 0.5886 time to fit residues: 91.2557 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 ASN A1266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138349 restraints weight = 10266.241| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.50 r_work: 0.3311 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9974 Z= 0.160 Angle : 0.547 9.242 13675 Z= 0.293 Chirality : 0.041 0.146 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.693 107.505 1834 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 4.14 % Allowed : 20.78 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.27), residues: 1026 helix: 1.80 (0.21), residues: 600 sheet: -1.19 (0.72), residues: 44 loop : 0.24 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.025 0.002 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 9970) covalent geometry : angle 0.54630 / 0.29 (13672) hydrogen bonds : bond 0.03895 / 2.63 ( 501) hydrogen bonds : angle 4.27022 / 3.15 ( 1456) metal coordination : bond 0.00925 / 0.37 ( 4) metal coordination : angle 1.79239 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.359 Fit side-chains REVERT: A 251 LYS cc_start: 0.7519 (mttt) cc_final: 0.7258 (mtmm) REVERT: A 271 LYS cc_start: 0.7413 (tttt) cc_final: 0.6818 (tmmt) REVERT: A 306 LYS cc_start: 0.7339 (ttpt) cc_final: 0.7098 (tttt) REVERT: A 474 ASP cc_start: 0.8117 (p0) cc_final: 0.7910 (p0) REVERT: A 571 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: A 732 LYS cc_start: 0.8201 (tppp) cc_final: 0.7727 (mtpt) REVERT: A 736 GLN cc_start: 0.8198 (pt0) cc_final: 0.7693 (mm110) REVERT: A 800 LYS cc_start: 0.8153 (pttt) cc_final: 0.7724 (ptmm) REVERT: A 908 MET cc_start: 0.7616 (ptm) cc_final: 0.7380 (ptm) REVERT: A 934 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7811 (tmtt) REVERT: A 972 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6718 (tppt) REVERT: A 975 LYS cc_start: 0.7752 (mttt) cc_final: 0.7274 (mmtp) REVERT: A 995 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7181 (mmm) REVERT: A 1002 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6563 (tpp) REVERT: A 1026 THR cc_start: 0.8105 (m) cc_final: 0.7702 (p) REVERT: A 1044 SER cc_start: 0.8634 (p) cc_final: 0.8377 (t) REVERT: A 1123 LYS cc_start: 0.7654 (mmtt) cc_final: 0.6952 (mtmp) REVERT: A 1155 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7660 (mtmt) REVERT: A 1171 ASP cc_start: 0.7740 (t0) cc_final: 0.7481 (m-30) REVERT: A 1210 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7533 (mp-120) REVERT: A 1264 THR cc_start: 0.8042 (m) cc_final: 0.7742 (p) outliers start: 39 outliers final: 14 residues processed: 142 average time/residue: 0.5513 time to fit residues: 84.0309 Evaluate side-chains 130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 102 optimal weight: 30.0000 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138291 restraints weight = 10174.244| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.48 r_work: 0.3233 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9974 Z= 0.156 Angle : 0.545 9.908 13675 Z= 0.292 Chirality : 0.041 0.155 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.691 106.872 1834 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 3.71 % Allowed : 21.42 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.27), residues: 1026 helix: 1.78 (0.21), residues: 600 sheet: -1.13 (0.72), residues: 44 loop : 0.22 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1132 TYR 0.018 0.002 TYR A 484 PHE 0.024 0.002 PHE A 605 TRP 0.009 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9970) covalent geometry : angle 0.54446 / 0.29 (13672) hydrogen bonds : bond 0.03865 / 2.61 ( 501) hydrogen bonds : angle 4.26847 / 3.16 ( 1456) metal coordination : bond 0.00967 / 0.39 ( 4) metal coordination : angle 1.63301 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.210 Fit side-chains REVERT: A 251 LYS cc_start: 0.7561 (mttt) cc_final: 0.7249 (mtmm) REVERT: A 271 LYS cc_start: 0.7468 (tttt) cc_final: 0.6889 (tmmt) REVERT: A 306 LYS cc_start: 0.7352 (ttpt) cc_final: 0.7105 (tttt) REVERT: A 550 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7799 (mtm-85) REVERT: A 571 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7687 (mm-40) REVERT: A 732 LYS cc_start: 0.8206 (tppp) cc_final: 0.7734 (mtpt) REVERT: A 736 GLN cc_start: 0.8192 (pt0) cc_final: 0.7707 (mm110) REVERT: A 800 LYS cc_start: 0.8155 (pttt) cc_final: 0.7735 (ptmm) REVERT: A 908 MET cc_start: 0.7564 (ptm) cc_final: 0.7301 (ptm) REVERT: A 934 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7833 (tmtt) REVERT: A 972 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6801 (tppt) REVERT: A 975 LYS cc_start: 0.7771 (mttt) cc_final: 0.7266 (mmtp) REVERT: A 995 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7150 (mmm) REVERT: A 1002 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6475 (tpp) REVERT: A 1026 THR cc_start: 0.8176 (m) cc_final: 0.7769 (p) REVERT: A 1044 SER cc_start: 0.8645 (p) cc_final: 0.8386 (t) REVERT: A 1123 LYS cc_start: 0.7694 (mmtt) cc_final: 0.6971 (mtmp) REVERT: A 1171 ASP cc_start: 0.7699 (t0) cc_final: 0.7456 (m-30) REVERT: A 1210 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7524 (mp-120) REVERT: A 1264 THR cc_start: 0.8025 (m) cc_final: 0.7730 (p) outliers start: 35 outliers final: 14 residues processed: 143 average time/residue: 0.5829 time to fit residues: 89.4437 Evaluate side-chains 130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 408 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137340 restraints weight = 10155.544| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.47 r_work: 0.3199 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9974 Z= 0.173 Angle : 0.562 9.996 13675 Z= 0.300 Chirality : 0.041 0.151 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.720 108.684 1834 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 4.35 % Allowed : 21.63 % Favored : 74.02 % 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: 1.48 (0.27), residues: 1026 helix: 1.74 (0.21), residues: 600 sheet: -1.09 (0.74), residues: 43 loop : 0.12 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.027 0.002 PHE A 605 TRP 0.009 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 9970) covalent geometry : angle 0.56157 / 0.30 (13672) hydrogen bonds : bond 0.03899 / 2.63 ( 501) hydrogen bonds : angle 4.29457 / 3.18 ( 1456) metal coordination : bond 0.01033 / 0.42 ( 4) metal coordination : angle 1.77813 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.457 Fit side-chains REVERT: A 251 LYS cc_start: 0.7555 (mttt) cc_final: 0.7227 (mtmm) REVERT: A 271 LYS cc_start: 0.7458 (tttt) cc_final: 0.7174 (mmtt) REVERT: A 298 LYS cc_start: 0.8159 (tptt) cc_final: 0.7553 (tppt) REVERT: A 306 LYS cc_start: 0.7366 (ttpt) cc_final: 0.7154 (tttt) REVERT: A 550 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7780 (mtm-85) REVERT: A 552 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8391 (mt0) REVERT: A 571 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7742 (mm-40) REVERT: A 732 LYS cc_start: 0.8223 (tppp) cc_final: 0.7739 (mtpt) REVERT: A 736 GLN cc_start: 0.8207 (pt0) cc_final: 0.7738 (mm110) REVERT: A 800 LYS cc_start: 0.8163 (pttt) cc_final: 0.7737 (ptmm) REVERT: A 908 MET cc_start: 0.7552 (ptm) cc_final: 0.7294 (ptm) REVERT: A 934 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7794 (tmtt) REVERT: A 972 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6842 (tppt) REVERT: A 975 LYS cc_start: 0.7783 (mttt) cc_final: 0.7274 (mmtp) REVERT: A 995 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7159 (mmm) REVERT: A 1002 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6529 (tpp) REVERT: A 1026 THR cc_start: 0.8186 (m) cc_final: 0.7803 (p) REVERT: A 1044 SER cc_start: 0.8669 (p) cc_final: 0.8377 (t) REVERT: A 1123 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7031 (mtmp) REVERT: A 1155 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7619 (mtmt) REVERT: A 1164 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 1171 ASP cc_start: 0.7782 (t0) cc_final: 0.7514 (m-30) REVERT: A 1210 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7934 (mp10) REVERT: A 1229 MET cc_start: 0.8803 (mmp) cc_final: 0.8571 (mmp) REVERT: A 1264 THR cc_start: 0.8032 (m) cc_final: 0.7736 (p) outliers start: 41 outliers final: 19 residues processed: 144 average time/residue: 0.5815 time to fit residues: 89.8370 Evaluate side-chains 136 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 408 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137637 restraints weight = 10183.306| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.53 r_work: 0.3277 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9974 Z= 0.143 Angle : 0.545 10.681 13675 Z= 0.292 Chirality : 0.040 0.144 1521 Planarity : 0.004 0.040 1514 Dihedral : 17.705 106.574 1834 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.92 % Allowed : 22.06 % Favored : 74.02 % 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: 1.52 (0.27), residues: 1026 helix: 1.78 (0.21), residues: 600 sheet: -1.09 (0.74), residues: 43 loop : 0.13 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1052 TYR 0.018 0.002 TYR A 484 PHE 0.023 0.002 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9970) covalent geometry : angle 0.54486 / 0.29 (13672) hydrogen bonds : bond 0.03816 / 2.59 ( 501) hydrogen bonds : angle 4.26743 / 3.17 ( 1456) metal coordination : bond 0.00862 / 0.34 ( 4) metal coordination : angle 1.64162 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.354 Fit side-chains REVERT: A 251 LYS cc_start: 0.7489 (mttt) cc_final: 0.7275 (mtmm) REVERT: A 271 LYS cc_start: 0.7430 (tttt) cc_final: 0.6795 (tmmt) REVERT: A 298 LYS cc_start: 0.8174 (tptt) cc_final: 0.7556 (tppt) REVERT: A 306 LYS cc_start: 0.7336 (ttpt) cc_final: 0.7122 (tttt) REVERT: A 550 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7783 (mtm-85) REVERT: A 571 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7699 (mm-40) REVERT: A 732 LYS cc_start: 0.8235 (tppp) cc_final: 0.7763 (mtpt) REVERT: A 736 GLN cc_start: 0.8210 (pt0) cc_final: 0.7734 (mm110) REVERT: A 800 LYS cc_start: 0.8149 (pttt) cc_final: 0.7716 (ptmm) REVERT: A 908 MET cc_start: 0.7551 (ptm) cc_final: 0.7316 (ptm) REVERT: A 934 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7850 (tmtt) REVERT: A 972 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6819 (tppt) REVERT: A 975 LYS cc_start: 0.7786 (mttt) cc_final: 0.7260 (mmtp) REVERT: A 995 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7142 (mmm) REVERT: A 1002 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6501 (tpp) REVERT: A 1026 THR cc_start: 0.8150 (m) cc_final: 0.7784 (p) REVERT: A 1044 SER cc_start: 0.8653 (p) cc_final: 0.8371 (t) REVERT: A 1123 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7086 (mtmp) REVERT: A 1155 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7635 (mtmt) REVERT: A 1164 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7305 (mp) REVERT: A 1171 ASP cc_start: 0.7721 (t0) cc_final: 0.7466 (m-30) REVERT: A 1210 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7928 (mp10) REVERT: A 1229 MET cc_start: 0.8807 (mmp) cc_final: 0.8561 (mmp) REVERT: A 1264 THR cc_start: 0.8023 (m) cc_final: 0.7726 (p) outliers start: 37 outliers final: 15 residues processed: 139 average time/residue: 0.5904 time to fit residues: 88.0526 Evaluate side-chains 130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 408 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138339 restraints weight = 10135.808| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.49 r_work: 0.3288 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9974 Z= 0.146 Angle : 0.551 11.033 13675 Z= 0.294 Chirality : 0.040 0.143 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.697 104.699 1834 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 3.29 % Allowed : 22.59 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.27), residues: 1026 helix: 1.77 (0.21), residues: 600 sheet: -1.06 (0.75), residues: 43 loop : 0.11 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1052 TYR 0.020 0.002 TYR A1086 PHE 0.024 0.002 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9970) covalent geometry : angle 0.55011 / 0.29 (13672) hydrogen bonds : bond 0.03786 / 2.56 ( 501) hydrogen bonds : angle 4.25352 / 3.16 ( 1456) metal coordination : bond 0.00870 / 0.35 ( 4) metal coordination : angle 1.71725 / 0.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.295 Fit side-chains REVERT: A 251 LYS cc_start: 0.7469 (mttt) cc_final: 0.7218 (mtmm) REVERT: A 271 LYS cc_start: 0.7420 (tttt) cc_final: 0.6775 (tmmt) REVERT: A 298 LYS cc_start: 0.8143 (tptt) cc_final: 0.7519 (tppt) REVERT: A 306 LYS cc_start: 0.7299 (ttpt) cc_final: 0.7094 (tttt) REVERT: A 550 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7855 (mtm-85) REVERT: A 571 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7717 (mm-40) REVERT: A 732 LYS cc_start: 0.8221 (tppp) cc_final: 0.7748 (mtpt) REVERT: A 736 GLN cc_start: 0.8205 (pt0) cc_final: 0.7741 (mm110) REVERT: A 800 LYS cc_start: 0.8138 (pttt) cc_final: 0.7718 (ptmm) REVERT: A 908 MET cc_start: 0.7556 (ptm) cc_final: 0.7262 (ptm) REVERT: A 934 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7859 (tmtt) REVERT: A 972 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6759 (tppt) REVERT: A 975 LYS cc_start: 0.7794 (mttt) cc_final: 0.7258 (mmtp) REVERT: A 995 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7146 (mmm) REVERT: A 1026 THR cc_start: 0.8129 (m) cc_final: 0.7769 (p) REVERT: A 1044 SER cc_start: 0.8645 (p) cc_final: 0.8361 (t) REVERT: A 1123 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7075 (mtmp) REVERT: A 1171 ASP cc_start: 0.7723 (t0) cc_final: 0.7457 (m-30) REVERT: A 1210 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7520 (mp-120) REVERT: A 1229 MET cc_start: 0.8777 (mmp) cc_final: 0.8516 (mmp) REVERT: A 1232 TYR cc_start: 0.8655 (m-80) cc_final: 0.8452 (m-80) REVERT: A 1264 THR cc_start: 0.7995 (m) cc_final: 0.7702 (p) outliers start: 31 outliers final: 14 residues processed: 133 average time/residue: 0.6097 time to fit residues: 86.7933 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1121 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 0.0670 chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138647 restraints weight = 10044.914| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.52 r_work: 0.3346 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9974 Z= 0.141 Angle : 0.552 11.939 13675 Z= 0.294 Chirality : 0.040 0.163 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.689 101.641 1834 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 2.33 % Allowed : 23.65 % Favored : 74.02 % 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: 1.51 (0.27), residues: 1026 helix: 1.78 (0.21), residues: 600 sheet: -1.36 (0.71), residues: 48 loop : 0.18 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 483 TYR 0.017 0.002 TYR A 484 PHE 0.023 0.001 PHE A 605 TRP 0.013 0.001 TRP A1247 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9970) covalent geometry : angle 0.55145 / 0.29 (13672) hydrogen bonds : bond 0.03743 / 2.54 ( 501) hydrogen bonds : angle 4.24731 / 3.15 ( 1456) metal coordination : bond 0.00808 / 0.32 ( 4) metal coordination : angle 1.69189 / 0.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.269 Fit side-chains REVERT: A 271 LYS cc_start: 0.7480 (tttt) cc_final: 0.6875 (tmmt) REVERT: A 298 LYS cc_start: 0.8094 (tptt) cc_final: 0.7553 (tppt) REVERT: A 306 LYS cc_start: 0.7433 (ttpt) cc_final: 0.7222 (tttt) REVERT: A 550 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7881 (mtm-85) REVERT: A 552 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: A 571 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: A 732 LYS cc_start: 0.8244 (tppp) cc_final: 0.7840 (mtpt) REVERT: A 736 GLN cc_start: 0.8193 (pt0) cc_final: 0.7765 (mm110) REVERT: A 800 LYS cc_start: 0.8159 (pttt) cc_final: 0.7774 (ptmm) REVERT: A 908 MET cc_start: 0.7567 (ptm) cc_final: 0.7237 (ptm) REVERT: A 972 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6784 (tppt) REVERT: A 975 LYS cc_start: 0.7790 (mttt) cc_final: 0.7285 (mmtp) REVERT: A 995 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7122 (mmm) REVERT: A 1002 MET cc_start: 0.6586 (mmp) cc_final: 0.6272 (tpp) REVERT: A 1026 THR cc_start: 0.8149 (m) cc_final: 0.7811 (p) REVERT: A 1044 SER cc_start: 0.8645 (p) cc_final: 0.8368 (t) REVERT: A 1123 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7228 (mtmp) REVERT: A 1171 ASP cc_start: 0.7737 (t0) cc_final: 0.7459 (m-30) REVERT: A 1210 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7607 (mp-120) REVERT: A 1229 MET cc_start: 0.8837 (mmp) cc_final: 0.8549 (mmp) REVERT: A 1264 THR cc_start: 0.8017 (m) cc_final: 0.7731 (p) outliers start: 22 outliers final: 12 residues processed: 125 average time/residue: 0.5432 time to fit residues: 72.3557 Evaluate side-chains 125 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1121 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137745 restraints weight = 10104.499| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.52 r_work: 0.3295 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9974 Z= 0.163 Angle : 0.567 12.247 13675 Z= 0.303 Chirality : 0.042 0.233 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.692 102.690 1832 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 23.44 % Favored : 73.70 % 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: 1.41 (0.27), residues: 1026 helix: 1.71 (0.21), residues: 600 sheet: -1.41 (0.70), residues: 48 loop : 0.11 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1086 PHE 0.025 0.002 PHE A 605 TRP 0.013 0.001 TRP A1247 HIS 0.004 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9970) covalent geometry : angle 0.56597 / 0.30 (13672) hydrogen bonds : bond 0.03791 / 2.57 ( 501) hydrogen bonds : angle 4.28338 / 3.18 ( 1456) metal coordination : bond 0.00872 / 0.35 ( 4) metal coordination : angle 1.80124 / 0.97 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3489.09 seconds wall clock time: 60 minutes 18.54 seconds (3618.54 seconds total)