Starting phenix.real_space_refine on Wed Aug 5 20:06:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkw_48340/08_2026/9mkw_48340.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 20 5.16 5 C 6967 2.51 5 N 1850 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 11190 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9852 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 1162} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 764 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 11, 'rna3p': 24} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 2.62, per 1000 atoms: 0.23 Number of scatterers: 11190 At special positions: 0 Unit cell: (109.22, 104.06, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 64 15.00 O 2289 8.00 N 1850 7.00 C 6967 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: 1.02 Conformation dependent library (CDL) restraints added in 522.8 milliseconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 54.0% alpha, 8.4% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 4.299A pdb=" N GLU A 6 " --> pdb=" O ILE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.251A pdb=" N ASN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.742A pdb=" N ASP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 87 removed outlier: 3.642A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.632A pdb=" N SER A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.411A pdb=" N LYS A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.954A pdb=" N ASN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.707A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.469A pdb=" N PHE A 182 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.830A pdb=" N ASP A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.503A pdb=" N PHE A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.819A pdb=" N LYS A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 319 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.549A pdb=" N VAL A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.627A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 474 through 506 Proline residue: A 486 - end of helix removed outlier: 3.797A pdb=" N GLN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.847A pdb=" N VAL A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 573 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.779A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 668 through 674 Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.316A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.502A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 731 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.791A pdb=" N ASP A 736 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 737 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.968A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 removed outlier: 3.532A pdb=" N GLN A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.796A pdb=" N PHE A 793 " --> pdb=" O ASN A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 removed outlier: 4.320A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.512A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.647A pdb=" N LEU A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 Processing helix chain 'A' and resid 977 through 997 removed outlier: 3.729A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1036 removed outlier: 4.156A pdb=" N LYS A1026 " --> pdb=" O GLN A1022 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1027 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A1028 " --> pdb=" O TYR A1024 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1067 Processing helix chain 'A' and resid 1101 through 1109 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.553A pdb=" N PHE A1133 " --> pdb=" O TYR A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1180 removed outlier: 4.162A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 4.159A pdb=" N GLY A1188 " --> pdb=" O TYR A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1198 removed outlier: 4.038A pdb=" N ALA A1194 " --> pdb=" O CYS A1190 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1215 removed outlier: 3.595A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1267 Processing helix chain 'A' and resid 1270 through 1275 Processing helix chain 'A' and resid 1287 through 1299 removed outlier: 3.623A pdb=" N ASN A1299 " --> pdb=" O VAL A1295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 597 removed outlier: 5.100A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 788 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA4, first strand: chain 'A' and resid 848 through 850 Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 940 removed outlier: 6.717A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 943 through 944 Processing sheet with id=AA7, first strand: chain 'A' and resid 1004 through 1006 Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AA9, first strand: chain 'A' and resid 1127 through 1128 446 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2557 1.33 - 1.45: 2685 1.45 - 1.57: 6142 1.57 - 1.69: 125 1.69 - 1.81: 32 Bond restraints: 11541 Sorted by residual: bond pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 bond pdb=" C3' DT C -12 " pdb=" C2' DT C -12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.84e+00 bond pdb=" C3' DG C -7 " pdb=" C2' DG C -7 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.95e+00 bond pdb=" C3' DA C 2 " pdb=" C2' DA C 2 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.83e+00 bond pdb=" C3' DA C -6 " pdb=" C2' DA C -6 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.77e+00 ... (remaining 11536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 15194 1.45 - 2.90: 530 2.90 - 4.35: 49 4.35 - 5.80: 12 5.80 - 7.25: 5 Bond angle restraints: 15790 Sorted by residual: angle pdb=" O4' DT C 1 " pdb=" C4' DT C 1 " pdb=" C3' DT C 1 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" O5' G B -9 " pdb=" C5' G B -9 " pdb=" C4' G B -9 " ideal model delta sigma weight residual 109.40 112.81 -3.41 8.00e-01 1.56e+00 1.81e+01 angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 1 " pdb=" C4 DT C 1 " pdb=" O4 DT C 1 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" O4' DG D 0 " pdb=" C4' DG D 0 " pdb=" C3' DG D 0 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 6410 26.22 - 52.43: 444 52.43 - 78.65: 107 78.65 - 104.87: 7 104.87 - 131.09: 1 Dihedral angle restraints: 6969 sinusoidal: 3436 harmonic: 3533 Sorted by residual: dihedral pdb=" C4' DA C -14 " pdb=" C3' DA C -14 " pdb=" O3' DA C -14 " pdb=" P DT C -13 " ideal model delta sinusoidal sigma weight residual -140.00 -8.91 -131.09 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" CA TYR A 392 " pdb=" C TYR A 392 " pdb=" N PHE A 393 " pdb=" CA PHE A 393 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS A 541 " pdb=" C LYS A 541 " pdb=" N ILE A 542 " pdb=" CA ILE A 542 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1707 0.126 - 0.251: 19 0.251 - 0.377: 0 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 1728 Sorted by residual: chirality pdb=" P DT D -4 " pdb=" OP1 DT D -4 " pdb=" OP2 DT D -4 " pdb=" O5' DT D -4 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" P DT D -3 " pdb=" OP1 DT D -3 " pdb=" OP2 DT D -3 " pdb=" O5' DT D -3 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CA VAL A 576 " pdb=" N VAL A 576 " pdb=" C VAL A 576 " pdb=" CB VAL A 576 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 1725 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1029 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C LYS A1029 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS A1029 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A1030 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 12 " 0.022 2.00e-02 2.50e+03 9.81e-03 2.65e+00 pdb=" N9 A B 12 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 12 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 12 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A B 12 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A B 12 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 12 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A B 12 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 485 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 486 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 486 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 486 " -0.023 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 719 2.73 - 3.27: 11797 3.27 - 3.81: 18835 3.81 - 4.36: 22095 4.36 - 4.90: 34758 Nonbonded interactions: 88204 Sorted by model distance: nonbonded pdb=" O2' A B 15 " pdb=" O4' A B 16 " model vdw 2.184 3.040 nonbonded pdb=" O ASN A 952 " pdb=" NZ LYS A 956 " model vdw 2.210 3.120 nonbonded pdb=" OE1 GLN A1094 " pdb=" OH TYR A1130 " model vdw 2.212 3.040 nonbonded pdb=" O ILE A 113 " pdb=" OG SER A 116 " model vdw 2.214 3.040 nonbonded pdb=" N TYR A 248 " pdb=" OD1 ASN A 268 " model vdw 2.233 3.120 ... (remaining 88199 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 0.037 11541 Z= 0.257 Angle : 0.614 7.254 15790 Z= 0.426 Chirality : 0.048 0.628 1728 Planarity : 0.003 0.040 1786 Dihedral : 17.578 131.086 4681 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1167 helix: 0.80 (0.23), residues: 542 sheet: -0.36 (0.52), residues: 103 loop : -1.26 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 186 TYR 0.023 0.002 TYR A1169 PHE 0.026 0.002 PHE A 244 TRP 0.022 0.002 TRP A1142 HIS 0.003 0.001 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.26 (11541) covalent geometry : angle 0.61443 / 0.43 (15790) hydrogen bonds : bond 0.14926 / 10.59 ( 484) hydrogen bonds : angle 5.91151 / 4.33 ( 1331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7777 (m-30) cc_final: 0.7570 (m-30) REVERT: A 60 PHE cc_start: 0.7972 (m-80) cc_final: 0.7633 (m-80) REVERT: A 92 ASP cc_start: 0.9323 (m-30) cc_final: 0.8933 (p0) REVERT: A 117 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7720 (tm-30) REVERT: A 753 PHE cc_start: 0.8007 (t80) cc_final: 0.7670 (t80) REVERT: A 899 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7788 (mp0) REVERT: A 984 TYR cc_start: 0.6796 (t80) cc_final: 0.6251 (t80) REVERT: A 1031 LEU cc_start: 0.8839 (tp) cc_final: 0.8601 (tp) REVERT: A 1217 MET cc_start: 0.7881 (mmm) cc_final: 0.7218 (tpp) REVERT: A 1290 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7752 (tp30) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1214 time to fit residues: 31.7658 Evaluate side-chains 97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN A 282 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.143370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105853 restraints weight = 48493.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.106637 restraints weight = 26211.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.107497 restraints weight = 17605.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.108208 restraints weight = 13610.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.108651 restraints weight = 12158.360| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11541 Z= 0.176 Angle : 0.637 14.454 15790 Z= 0.352 Chirality : 0.042 0.189 1728 Planarity : 0.004 0.046 1786 Dihedral : 17.899 130.672 2126 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.48 % Allowed : 10.70 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.24), residues: 1167 helix: 0.44 (0.22), residues: 542 sheet: -0.29 (0.53), residues: 101 loop : -1.13 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 872 TYR 0.021 0.002 TYR A 659 PHE 0.021 0.002 PHE A 244 TRP 0.005 0.001 TRP A1142 HIS 0.006 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (11541) covalent geometry : angle 0.63728 / 0.35 (15790) hydrogen bonds : bond 0.05296 / 3.48 ( 484) hydrogen bonds : angle 5.24452 / 3.73 ( 1331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7431 (mtm180) REVERT: A 92 ASP cc_start: 0.9487 (m-30) cc_final: 0.9016 (p0) REVERT: A 96 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9343 (ptmm) REVERT: A 117 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7727 (tm-30) REVERT: A 213 GLU cc_start: 0.9319 (tp30) cc_final: 0.9036 (tm-30) REVERT: A 301 ASN cc_start: 0.8782 (m-40) cc_final: 0.8541 (m110) REVERT: A 753 PHE cc_start: 0.7997 (t80) cc_final: 0.7657 (t80) REVERT: A 899 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 941 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7923 (t80) REVERT: A 984 TYR cc_start: 0.7071 (t80) cc_final: 0.6632 (t80) REVERT: A 1077 VAL cc_start: 0.8056 (p) cc_final: 0.7677 (m) REVERT: A 1217 MET cc_start: 0.7399 (mmm) cc_final: 0.6882 (tpp) REVERT: A 1290 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7814 (tp30) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.1032 time to fit residues: 18.0435 Evaluate side-chains 113 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 62 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.141287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.103921 restraints weight = 49609.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.104460 restraints weight = 27651.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.105197 restraints weight = 18777.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.106011 restraints weight = 15333.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.106374 restraints weight = 13301.657| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11541 Z= 0.200 Angle : 0.620 10.380 15790 Z= 0.347 Chirality : 0.042 0.179 1728 Planarity : 0.004 0.044 1786 Dihedral : 18.013 132.277 2126 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.12 % Allowed : 13.65 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1167 helix: 0.08 (0.21), residues: 553 sheet: -0.36 (0.53), residues: 99 loop : -1.31 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.029 0.002 TYR A 659 PHE 0.018 0.002 PHE A 244 TRP 0.009 0.002 TRP A 609 HIS 0.008 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (11541) covalent geometry : angle 0.62007 / 0.35 (15790) hydrogen bonds : bond 0.05272 / 3.42 ( 484) hydrogen bonds : angle 5.15859 / 3.65 ( 1331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7801 (mtm180) cc_final: 0.6819 (mtm180) REVERT: A 92 ASP cc_start: 0.9571 (m-30) cc_final: 0.9143 (p0) REVERT: A 117 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7734 (tm-30) REVERT: A 245 ASP cc_start: 0.7960 (m-30) cc_final: 0.7306 (p0) REVERT: A 753 PHE cc_start: 0.8043 (t80) cc_final: 0.7696 (t80) REVERT: A 899 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 941 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 984 TYR cc_start: 0.7252 (t80) cc_final: 0.6824 (t80) REVERT: A 1217 MET cc_start: 0.7411 (mmm) cc_final: 0.6856 (tpp) outliers start: 23 outliers final: 19 residues processed: 118 average time/residue: 0.0969 time to fit residues: 16.9986 Evaluate side-chains 111 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 45 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN A1261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105499 restraints weight = 48103.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.107274 restraints weight = 25803.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.108429 restraints weight = 17291.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.108891 restraints weight = 13529.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.109464 restraints weight = 11998.179| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11541 Z= 0.124 Angle : 0.551 9.701 15790 Z= 0.310 Chirality : 0.040 0.212 1728 Planarity : 0.004 0.045 1786 Dihedral : 17.915 132.866 2126 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.03 % Allowed : 15.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1167 helix: 0.20 (0.21), residues: 553 sheet: -0.34 (0.54), residues: 88 loop : -1.22 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 746 TYR 0.020 0.001 TYR A 659 PHE 0.024 0.001 PHE A 269 TRP 0.006 0.001 TRP A 808 HIS 0.007 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (11541) covalent geometry : angle 0.55097 / 0.31 (15790) hydrogen bonds : bond 0.04612 / 3.02 ( 484) hydrogen bonds : angle 4.89437 / 3.46 ( 1331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7772 (mtm180) cc_final: 0.6731 (mtm180) REVERT: A 92 ASP cc_start: 0.9594 (m-30) cc_final: 0.9134 (p0) REVERT: A 96 LYS cc_start: 0.9601 (ptmm) cc_final: 0.9378 (pptt) REVERT: A 117 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7704 (tm-30) REVERT: A 245 ASP cc_start: 0.7880 (m-30) cc_final: 0.7251 (p0) REVERT: A 724 TYR cc_start: 0.8416 (m-10) cc_final: 0.8159 (m-80) REVERT: A 753 PHE cc_start: 0.7889 (t80) cc_final: 0.7586 (t80) REVERT: A 895 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8112 (mmmm) REVERT: A 899 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 941 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 984 TYR cc_start: 0.7099 (t80) cc_final: 0.6712 (t80) REVERT: A 1067 MET cc_start: 0.8288 (ttt) cc_final: 0.8043 (ttt) REVERT: A 1217 MET cc_start: 0.7510 (mmm) cc_final: 0.7009 (tpp) REVERT: A 1281 LYS cc_start: 0.8722 (pptt) cc_final: 0.8450 (pptt) outliers start: 22 outliers final: 15 residues processed: 118 average time/residue: 0.1019 time to fit residues: 17.7998 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 282 ASN A 825 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** 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 = 0.4359 r_free = 0.4359 target = 0.138874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.102198 restraints weight = 49826.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.102560 restraints weight = 28666.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.103278 restraints weight = 19275.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104085 restraints weight = 15685.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104340 restraints weight = 13574.713| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11541 Z= 0.242 Angle : 0.654 10.886 15790 Z= 0.364 Chirality : 0.043 0.250 1728 Planarity : 0.004 0.042 1786 Dihedral : 18.146 132.707 2126 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.23 % Allowed : 17.44 % Favored : 79.34 % 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: -1.06 (0.23), residues: 1167 helix: 0.00 (0.21), residues: 562 sheet: -0.61 (0.55), residues: 88 loop : -1.47 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 297 TYR 0.021 0.002 TYR A 659 PHE 0.019 0.002 PHE A 244 TRP 0.012 0.002 TRP A 175 HIS 0.011 0.002 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 (11541) covalent geometry : angle 0.65413 / 0.36 (15790) hydrogen bonds : bond 0.05615 / 3.61 ( 484) hydrogen bonds : angle 5.11643 / 3.61 ( 1331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.9613 (m-30) cc_final: 0.9167 (p0) REVERT: A 117 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7733 (tm-30) REVERT: A 183 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7628 (m170) REVERT: A 245 ASP cc_start: 0.8011 (m-30) cc_final: 0.7425 (p0) REVERT: A 269 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: A 899 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 941 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 984 TYR cc_start: 0.7417 (t80) cc_final: 0.6999 (t80) REVERT: A 1217 MET cc_start: 0.7413 (mmm) cc_final: 0.6826 (tpp) outliers start: 35 outliers final: 24 residues processed: 112 average time/residue: 0.1033 time to fit residues: 17.0531 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.102825 restraints weight = 48503.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.104240 restraints weight = 26401.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.105057 restraints weight = 17673.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.106000 restraints weight = 14307.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106350 restraints weight = 12304.454| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11541 Z= 0.160 Angle : 0.584 8.567 15790 Z= 0.329 Chirality : 0.041 0.281 1728 Planarity : 0.004 0.063 1786 Dihedral : 18.084 132.180 2126 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.95 % Allowed : 17.62 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.23), residues: 1167 helix: 0.05 (0.21), residues: 562 sheet: -0.58 (0.55), residues: 86 loop : -1.44 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 746 TYR 0.021 0.002 TYR A 83 PHE 0.017 0.002 PHE A1240 TRP 0.007 0.001 TRP A 808 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (11541) covalent geometry : angle 0.58408 / 0.33 (15790) hydrogen bonds : bond 0.05001 / 3.22 ( 484) hydrogen bonds : angle 4.98585 / 3.51 ( 1331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9305 (m110) cc_final: 0.9037 (p0) REVERT: A 117 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7733 (tm-30) REVERT: A 183 HIS cc_start: 0.7883 (m170) cc_final: 0.7505 (m170) REVERT: A 245 ASP cc_start: 0.8063 (m-30) cc_final: 0.7528 (p0) REVERT: A 895 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8193 (mmmm) REVERT: A 899 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 941 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8211 (t80) REVERT: A 984 TYR cc_start: 0.7288 (t80) cc_final: 0.6835 (t80) REVERT: A 1067 MET cc_start: 0.8426 (ttt) cc_final: 0.8198 (ttt) REVERT: A 1217 MET cc_start: 0.7465 (mmm) cc_final: 0.6910 (tpp) REVERT: A 1261 HIS cc_start: 0.8315 (m90) cc_final: 0.7971 (p90) outliers start: 32 outliers final: 22 residues processed: 113 average time/residue: 0.0961 time to fit residues: 16.4758 Evaluate side-chains 109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 84 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.103834 restraints weight = 49358.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.105026 restraints weight = 27880.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.105831 restraints weight = 18579.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106667 restraints weight = 15045.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106928 restraints weight = 13049.079| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11541 Z= 0.142 Angle : 0.581 8.206 15790 Z= 0.326 Chirality : 0.041 0.304 1728 Planarity : 0.004 0.055 1786 Dihedral : 18.016 131.988 2126 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.49 % Allowed : 18.63 % Favored : 78.87 % 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: -0.91 (0.23), residues: 1167 helix: 0.12 (0.21), residues: 559 sheet: -0.66 (0.55), residues: 88 loop : -1.34 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.021 0.002 TYR A 83 PHE 0.025 0.002 PHE A 269 TRP 0.007 0.001 TRP A 808 HIS 0.004 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11541) covalent geometry : angle 0.58077 / 0.33 (15790) hydrogen bonds : bond 0.04840 / 3.12 ( 484) hydrogen bonds : angle 4.90976 / 3.45 ( 1331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7767 (mtm180) cc_final: 0.6610 (mtm180) REVERT: A 78 ASN cc_start: 0.9312 (m110) cc_final: 0.9062 (p0) REVERT: A 117 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7733 (tm-30) REVERT: A 182 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 183 HIS cc_start: 0.7827 (m170) cc_final: 0.7487 (m170) REVERT: A 245 ASP cc_start: 0.8050 (m-30) cc_final: 0.7606 (p0) REVERT: A 895 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8204 (mmmm) REVERT: A 899 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 941 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 984 TYR cc_start: 0.7293 (t80) cc_final: 0.6843 (t80) REVERT: A 1217 MET cc_start: 0.7598 (mmm) cc_final: 0.7074 (tpp) REVERT: A 1261 HIS cc_start: 0.8285 (m90) cc_final: 0.7957 (p-80) outliers start: 27 outliers final: 22 residues processed: 107 average time/residue: 0.0929 time to fit residues: 15.1810 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 0.0670 chunk 78 optimal weight: 0.0570 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 90 optimal weight: 0.0770 chunk 29 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105515 restraints weight = 48564.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.106877 restraints weight = 26762.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.107667 restraints weight = 18190.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.108639 restraints weight = 14714.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.108859 restraints weight = 12650.542| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11541 Z= 0.119 Angle : 0.565 8.417 15790 Z= 0.315 Chirality : 0.041 0.313 1728 Planarity : 0.003 0.046 1786 Dihedral : 17.923 131.823 2126 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.12 % Allowed : 19.28 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1167 helix: 0.24 (0.21), residues: 561 sheet: -0.67 (0.54), residues: 90 loop : -1.34 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.019 0.001 TYR A 83 PHE 0.022 0.001 PHE A 269 TRP 0.007 0.001 TRP A 808 HIS 0.003 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (11541) covalent geometry : angle 0.56498 / 0.32 (15790) hydrogen bonds : bond 0.04580 / 2.98 ( 484) hydrogen bonds : angle 4.75214 / 3.33 ( 1331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9321 (m110) cc_final: 0.9075 (p0) REVERT: A 92 ASP cc_start: 0.9620 (m-30) cc_final: 0.8932 (p0) REVERT: A 117 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7747 (tm-30) REVERT: A 182 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7868 (t80) REVERT: A 245 ASP cc_start: 0.7835 (m-30) cc_final: 0.7424 (p0) REVERT: A 301 ASN cc_start: 0.8585 (m-40) cc_final: 0.8190 (m-40) REVERT: A 753 PHE cc_start: 0.7916 (t80) cc_final: 0.7538 (t80) REVERT: A 895 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8200 (mmmm) REVERT: A 899 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 941 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8138 (t80) REVERT: A 984 TYR cc_start: 0.7202 (t80) cc_final: 0.6778 (t80) REVERT: A 1067 MET cc_start: 0.8137 (ttt) cc_final: 0.7835 (ttm) REVERT: A 1217 MET cc_start: 0.7632 (mmm) cc_final: 0.7266 (mmm) outliers start: 23 outliers final: 19 residues processed: 115 average time/residue: 0.0937 time to fit residues: 16.5187 Evaluate side-chains 109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1031 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 121 optimal weight: 50.0000 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 0.0040 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 535 ASN A 881 HIS ** A1257 ASN ** 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 = 0.4408 r_free = 0.4408 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104519 restraints weight = 48712.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.105914 restraints weight = 26872.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.106686 restraints weight = 18277.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.107546 restraints weight = 15011.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.107752 restraints weight = 12944.264| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11541 Z= 0.135 Angle : 0.587 11.544 15790 Z= 0.324 Chirality : 0.042 0.302 1728 Planarity : 0.003 0.043 1786 Dihedral : 17.908 131.438 2126 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.31 % Allowed : 20.39 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1167 helix: 0.27 (0.21), residues: 558 sheet: -0.66 (0.55), residues: 90 loop : -1.34 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.020 0.001 TYR A 83 PHE 0.022 0.001 PHE A 98 TRP 0.005 0.001 TRP A 808 HIS 0.004 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (11541) covalent geometry : angle 0.58726 / 0.32 (15790) hydrogen bonds : bond 0.04650 / 2.99 ( 484) hydrogen bonds : angle 4.77574 / 3.35 ( 1331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8091 (m-30) REVERT: A 78 ASN cc_start: 0.9335 (m110) cc_final: 0.9098 (p0) REVERT: A 117 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7755 (tm-30) REVERT: A 182 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7873 (t80) REVERT: A 245 ASP cc_start: 0.7864 (m-30) cc_final: 0.7486 (p0) REVERT: A 301 ASN cc_start: 0.8476 (m110) cc_final: 0.8093 (m110) REVERT: A 895 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8233 (mmmm) REVERT: A 899 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 941 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 984 TYR cc_start: 0.7269 (t80) cc_final: 0.6821 (t80) REVERT: A 1067 MET cc_start: 0.8162 (ttt) cc_final: 0.7830 (ttm) REVERT: A 1217 MET cc_start: 0.7669 (mmm) cc_final: 0.7290 (mmm) outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.0889 time to fit residues: 14.6455 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 95 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN A1257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.136286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.099649 restraints weight = 50323.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.100373 restraints weight = 28734.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.101378 restraints weight = 19637.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.101952 restraints weight = 15675.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.102128 restraints weight = 13833.892| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11541 Z= 0.326 Angle : 0.788 12.015 15790 Z= 0.434 Chirality : 0.047 0.316 1728 Planarity : 0.005 0.065 1786 Dihedral : 18.283 128.938 2126 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.68 % Allowed : 20.02 % Favored : 77.31 % 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 (0.23), residues: 1167 helix: -0.30 (0.21), residues: 556 sheet: -0.89 (0.55), residues: 86 loop : -1.58 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 746 TYR 0.027 0.003 TYR A1260 PHE 0.022 0.003 PHE A 737 TRP 0.026 0.004 TRP A 175 HIS 0.011 0.002 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.33 (11541) covalent geometry : angle 0.78758 / 0.43 (15790) hydrogen bonds : bond 0.06326 / 4.03 ( 484) hydrogen bonds : angle 5.38198 / 3.80 ( 1331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9354 (m110) cc_final: 0.9128 (p0) REVERT: A 92 ASP cc_start: 0.9252 (p0) cc_final: 0.8895 (p0) REVERT: A 117 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7745 (tm-30) REVERT: A 182 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 183 HIS cc_start: 0.8046 (m170) cc_final: 0.7720 (m170) REVERT: A 245 ASP cc_start: 0.8121 (m-30) cc_final: 0.7459 (p0) REVERT: A 633 MET cc_start: 0.9059 (pmm) cc_final: 0.8653 (pmm) REVERT: A 941 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 1217 MET cc_start: 0.7432 (mmm) cc_final: 0.6705 (tpp) outliers start: 29 outliers final: 22 residues processed: 104 average time/residue: 0.0903 time to fit residues: 14.2874 Evaluate side-chains 106 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 823 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 941 PHE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 649 ASN A 825 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105801 restraints weight = 47702.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.106532 restraints weight = 26011.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.107417 restraints weight = 17388.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108138 restraints weight = 13428.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.108622 restraints weight = 11913.483| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11541 Z= 0.131 Angle : 0.630 12.181 15790 Z= 0.345 Chirality : 0.042 0.346 1728 Planarity : 0.004 0.043 1786 Dihedral : 18.050 127.692 2126 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.85 % Allowed : 20.76 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1167 helix: 0.08 (0.21), residues: 554 sheet: -0.65 (0.56), residues: 88 loop : -1.38 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 746 TYR 0.017 0.001 TYR A 659 PHE 0.030 0.002 PHE A 98 TRP 0.010 0.001 TRP A 808 HIS 0.012 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (11541) covalent geometry : angle 0.62958 / 0.34 (15790) hydrogen bonds : bond 0.04814 / 3.12 ( 484) hydrogen bonds : angle 4.90414 / 3.42 ( 1331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.81 seconds wall clock time: 63 minutes 30.84 seconds (3810.84 seconds total)