Starting phenix.real_space_refine on Fri Jul 3 02:13:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkw_48340/07_2026/9mkw_48340.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkw_48340/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkw_48340/07_2026/9mkw_48340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkw_48340/07_2026/9mkw_48340.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkw_48340/07_2026/9mkw_48340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkw_48340/07_2026/9mkw_48340.cif" } 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-dev-6108/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: 2.82, per 1000 atoms: 0.25 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: 0.70 Conformation dependent library (CDL) restraints added in 470.7 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: 1.11 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: 2.20 Time building geometry restraints manager: 1.00 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: 15275 1.45 - 2.90: 456 2.90 - 4.35: 42 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=" 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 angle pdb=" N3 DT C -4 " pdb=" C4 DT C -4 " pdb=" O4 DT C -4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+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: 1719 0.126 - 0.251: 7 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: 1.490 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- 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= 0.254 Angle : 0.588 7.254 15790 Z= 0.402 Chirality : 0.045 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 0.00383 / 0.25 (11541) covalent geometry : angle 0.58808 / 0.40 (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 : 0.394 Fit side-chains 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: 0.1116 time to fit residues: 29.0533 Evaluate side-chains 96 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104708 restraints weight = 47516.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.106443 restraints weight = 26046.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.107234 restraints weight = 17560.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.108080 restraints weight = 14281.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.108297 restraints weight = 12272.131| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11541 Z= 0.178 Angle : 0.626 14.081 15790 Z= 0.349 Chirality : 0.041 0.187 1728 Planarity : 0.004 0.046 1786 Dihedral : 17.902 130.251 2126 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.38 % Allowed : 10.70 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1167 helix: 0.47 (0.22), residues: 542 sheet: -0.31 (0.53), residues: 101 loop : -1.12 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 872 TYR 0.020 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 0.00372 / 0.18 (11541) covalent geometry : angle 0.62601 / 0.35 (15790) hydrogen bonds : bond 0.05480 / 3.62 ( 484) hydrogen bonds : angle 5.26251 / 3.75 ( 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 123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.9532 (m-30) cc_final: 0.9061 (p0) REVERT: A 96 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9327 (ptmm) REVERT: A 117 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7735 (tm-30) REVERT: A 213 GLU cc_start: 0.9322 (tp30) cc_final: 0.9044 (tm-30) REVERT: A 301 ASN cc_start: 0.8764 (m-40) cc_final: 0.8521 (m110) REVERT: A 753 PHE cc_start: 0.8001 (t80) cc_final: 0.7659 (t80) REVERT: A 899 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 941 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 984 TYR cc_start: 0.7021 (t80) cc_final: 0.6546 (t80) REVERT: A 1217 MET cc_start: 0.7468 (mmm) cc_final: 0.6921 (tpp) REVERT: A 1290 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7840 (tp30) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.1010 time to fit residues: 17.2836 Evaluate side-chains 109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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: 20.0000 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: 0.8980 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.140893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.102637 restraints weight = 48429.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104131 restraints weight = 26640.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.105249 restraints weight = 17801.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.105699 restraints weight = 13952.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.106186 restraints weight = 12390.864| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11541 Z= 0.209 Angle : 0.627 10.706 15790 Z= 0.351 Chirality : 0.041 0.177 1728 Planarity : 0.004 0.044 1786 Dihedral : 18.030 131.833 2126 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.21 % Allowed : 13.47 % Favored : 84.32 % 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: -0.82 (0.23), residues: 1167 helix: 0.18 (0.21), residues: 550 sheet: -0.32 (0.53), residues: 99 loop : -1.33 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 746 TYR 0.030 0.002 TYR A 659 PHE 0.019 0.002 PHE A 244 TRP 0.009 0.002 TRP A 609 HIS 0.007 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (11541) covalent geometry : angle 0.62681 / 0.35 (15790) hydrogen bonds : bond 0.05335 / 3.48 ( 484) hydrogen bonds : angle 5.19462 / 3.68 ( 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 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.9541 (m-30) cc_final: 0.9079 (p0) REVERT: A 117 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7780 (tm-30) REVERT: A 245 ASP cc_start: 0.7985 (m-30) cc_final: 0.7325 (p0) REVERT: A 899 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 941 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8008 (t80) REVERT: A 984 TYR cc_start: 0.7218 (t80) cc_final: 0.6774 (t80) REVERT: A 1217 MET cc_start: 0.7436 (mmm) cc_final: 0.6879 (tpp) outliers start: 24 outliers final: 19 residues processed: 114 average time/residue: 0.1016 time to fit residues: 17.0927 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 : 0.369 ------------------------------------------------------------------------------- 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 183 HIS 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: 0.7980 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 6 optimal weight: 0.0970 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.143145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.104583 restraints weight = 49064.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.105991 restraints weight = 26989.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.106766 restraints weight = 18286.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.107810 restraints weight = 14911.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.108140 restraints weight = 12876.302| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11541 Z= 0.137 Angle : 0.557 9.810 15790 Z= 0.315 Chirality : 0.040 0.217 1728 Planarity : 0.004 0.046 1786 Dihedral : 17.958 132.744 2126 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.94 % Allowed : 16.14 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1167 helix: 0.27 (0.22), residues: 547 sheet: -0.23 (0.55), residues: 86 loop : -1.27 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.021 0.001 TYR A 659 PHE 0.017 0.001 PHE A1240 TRP 0.006 0.001 TRP A 808 HIS 0.008 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (11541) covalent geometry : angle 0.55665 / 0.31 (15790) hydrogen bonds : bond 0.04736 / 3.11 ( 484) hydrogen bonds : angle 4.94591 / 3.50 ( 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 126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.9560 (m-30) cc_final: 0.9133 (p0) REVERT: A 117 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7669 (tm-30) REVERT: A 245 ASP cc_start: 0.7892 (m-30) cc_final: 0.7431 (p0) REVERT: A 753 PHE cc_start: 0.7942 (t80) cc_final: 0.7612 (t80) REVERT: A 899 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 941 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 984 TYR cc_start: 0.7075 (t80) cc_final: 0.6657 (t80) REVERT: A 1067 MET cc_start: 0.8282 (ttt) cc_final: 0.8046 (ttt) REVERT: A 1217 MET cc_start: 0.7496 (mmm) cc_final: 0.6993 (tpp) REVERT: A 1281 LYS cc_start: 0.8734 (pptt) cc_final: 0.8471 (pptt) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.0938 time to fit residues: 16.0703 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 257 VAL 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 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 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=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: 8.9990 chunk 73 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 ASN A 282 ASN A 825 ASN A1261 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.100459 restraints weight = 50353.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.101096 restraints weight = 28319.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102099 restraints weight = 19459.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.102727 restraints weight = 15552.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.103054 restraints weight = 13671.777| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11541 Z= 0.274 Angle : 0.689 8.011 15790 Z= 0.387 Chirality : 0.044 0.270 1728 Planarity : 0.005 0.051 1786 Dihedral : 18.260 132.471 2126 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.87 % Allowed : 16.79 % 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: -1.28 (0.23), residues: 1167 helix: -0.22 (0.21), residues: 564 sheet: -0.64 (0.54), residues: 96 loop : -1.55 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 18 TYR 0.021 0.002 TYR A 659 PHE 0.022 0.003 PHE A 737 TRP 0.014 0.003 TRP A 175 HIS 0.009 0.002 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.27 (11541) covalent geometry : angle 0.68939 / 0.39 (15790) hydrogen bonds : bond 0.06026 / 3.88 ( 484) hydrogen bonds : angle 5.31005 / 3.76 ( 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 134 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7738 (tm-30) REVERT: A 183 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7711 (m170) REVERT: A 245 ASP cc_start: 0.8173 (m-30) cc_final: 0.7485 (p0) REVERT: A 269 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: A 895 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8548 (mmtm) REVERT: A 941 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 1217 MET cc_start: 0.7331 (mmm) cc_final: 0.6731 (tpp) outliers start: 42 outliers final: 29 residues processed: 120 average time/residue: 0.0840 time to fit residues: 15.1999 Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 109 ILE 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 208 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 257 VAL 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 274 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 633 MET 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 895 LYS 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: 10.0000 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 112 optimal weight: 0.0370 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 301 ASN A 649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.140276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.103238 restraints weight = 50238.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.103829 restraints weight = 27811.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.104563 restraints weight = 18709.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.105392 restraints weight = 15226.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.105778 restraints weight = 13012.274| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11541 Z= 0.160 Angle : 0.595 9.520 15790 Z= 0.335 Chirality : 0.042 0.297 1728 Planarity : 0.004 0.042 1786 Dihedral : 18.161 132.127 2126 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.86 % Allowed : 18.45 % Favored : 78.69 % 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: -1.12 (0.23), residues: 1167 helix: -0.05 (0.21), residues: 561 sheet: -0.54 (0.56), residues: 86 loop : -1.51 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.026 0.002 TYR A 83 PHE 0.018 0.002 PHE A1240 TRP 0.008 0.001 TRP A 808 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (11541) covalent geometry : angle 0.59498 / 0.34 (15790) hydrogen bonds : bond 0.05132 / 3.33 ( 484) hydrogen bonds : angle 5.09982 / 3.59 ( 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 121 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7744 (tm-30) REVERT: A 182 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7902 (t80) REVERT: A 183 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7650 (m170) REVERT: A 245 ASP cc_start: 0.8064 (m-30) cc_final: 0.7537 (p0) REVERT: A 269 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 941 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (t80) REVERT: A 1217 MET cc_start: 0.7404 (mmm) cc_final: 0.6857 (tpp) REVERT: A 1281 LYS cc_start: 0.8640 (pptt) cc_final: 0.8297 (pptt) outliers start: 31 outliers final: 21 residues processed: 109 average time/residue: 0.0942 time to fit residues: 15.5513 Evaluate side-chains 111 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 183 HIS 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 271 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 823 LYS 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 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: 5.9990 chunk 79 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 121 optimal weight: 50.0000 chunk 52 optimal weight: 0.0020 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4387 r_free = 0.4387 target = 0.141380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.103346 restraints weight = 49502.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104617 restraints weight = 27693.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.105709 restraints weight = 18581.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.106162 restraints weight = 14650.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106592 restraints weight = 12825.458| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2697 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= 0.137 Angle : 0.572 8.888 15790 Z= 0.323 Chirality : 0.041 0.320 1728 Planarity : 0.004 0.043 1786 Dihedral : 18.065 132.158 2126 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.94 % Allowed : 19.83 % Favored : 78.23 % 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: -0.96 (0.23), residues: 1167 helix: 0.08 (0.21), residues: 562 sheet: -0.51 (0.56), residues: 86 loop : -1.40 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.019 0.002 TYR A1096 PHE 0.019 0.002 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 0.00281 / 0.14 (11541) covalent geometry : angle 0.57207 / 0.32 (15790) hydrogen bonds : bond 0.04843 / 3.13 ( 484) hydrogen bonds : angle 4.96795 / 3.49 ( 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 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7725 (tm-30) REVERT: A 182 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 183 HIS cc_start: 0.7874 (m170) cc_final: 0.7561 (m170) REVERT: A 245 ASP cc_start: 0.8041 (m-30) cc_final: 0.7606 (p0) REVERT: A 899 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 941 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 1067 MET cc_start: 0.8372 (ttt) cc_final: 0.8167 (ttt) REVERT: A 1136 LYS cc_start: 0.6399 (ptmm) cc_final: 0.6179 (ptmm) REVERT: A 1217 MET cc_start: 0.7501 (mmm) cc_final: 0.6986 (tpp) outliers start: 21 outliers final: 15 residues processed: 106 average time/residue: 0.1033 time to fit residues: 16.5498 Evaluate side-chains 103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 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 182 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 266 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 823 LYS Chi-restraints excluded: chain A residue 903 LEU 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: 2.9990 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 0.0050 chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4382 r_free = 0.4382 target = 0.140699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103602 restraints weight = 49098.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.104286 restraints weight = 27724.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.105419 restraints weight = 18805.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.105840 restraints weight = 14617.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.106329 restraints weight = 13029.936| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11541 Z= 0.165 Angle : 0.596 8.585 15790 Z= 0.335 Chirality : 0.041 0.331 1728 Planarity : 0.004 0.043 1786 Dihedral : 18.059 131.858 2126 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.77 % Allowed : 19.46 % Favored : 77.77 % 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: 562 sheet: -0.54 (0.56), residues: 86 loop : -1.43 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 18 TYR 0.018 0.002 TYR A 659 PHE 0.018 0.002 PHE A1240 TRP 0.007 0.001 TRP A 609 HIS 0.008 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (11541) covalent geometry : angle 0.59604 / 0.34 (15790) hydrogen bonds : bond 0.05005 / 3.22 ( 484) hydrogen bonds : angle 4.95110 / 3.48 ( 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 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7708 (tm-30) REVERT: A 182 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7806 (t80) REVERT: A 183 HIS cc_start: 0.7893 (m170) cc_final: 0.7590 (m170) REVERT: A 245 ASP cc_start: 0.8015 (m-30) cc_final: 0.7667 (p0) REVERT: A 895 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8596 (mmtm) REVERT: A 899 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 941 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 1136 LYS cc_start: 0.6408 (ptmm) cc_final: 0.6185 (ptmm) REVERT: A 1217 MET cc_start: 0.7507 (mmm) cc_final: 0.6971 (tpp) REVERT: A 1261 HIS cc_start: 0.8052 (m90) cc_final: 0.7837 (p-80) outliers start: 30 outliers final: 26 residues processed: 106 average time/residue: 0.0999 time to fit residues: 15.7708 Evaluate side-chains 116 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 194 ASP 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 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 777 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 895 LYS 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 Chi-restraints excluded: chain A residue 1286 ILE 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: 2.9990 chunk 43 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 121 optimal weight: 40.0000 chunk 93 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4367 r_free = 0.4367 target = 0.139577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.102494 restraints weight = 49244.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103270 restraints weight = 27614.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.104004 restraints weight = 18773.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.104764 restraints weight = 15385.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.104980 restraints weight = 13382.706| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11541 Z= 0.193 Angle : 0.622 10.906 15790 Z= 0.347 Chirality : 0.042 0.340 1728 Planarity : 0.004 0.042 1786 Dihedral : 18.126 130.799 2126 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.04 % Allowed : 19.65 % 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: -1.03 (0.23), residues: 1167 helix: 0.05 (0.21), residues: 557 sheet: -0.59 (0.57), residues: 86 loop : -1.46 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.019 0.002 TYR A 659 PHE 0.016 0.002 PHE A1240 TRP 0.010 0.002 TRP A1142 HIS 0.006 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (11541) covalent geometry : angle 0.62194 / 0.35 (15790) hydrogen bonds : bond 0.05223 / 3.35 ( 484) hydrogen bonds : angle 5.03087 / 3.54 ( 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 120 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7729 (tm-30) REVERT: A 182 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 183 HIS cc_start: 0.7901 (m170) cc_final: 0.7625 (m170) REVERT: A 245 ASP cc_start: 0.8070 (m-30) cc_final: 0.7413 (p0) REVERT: A 899 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7786 (mt-10) REVERT: A 941 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (t80) REVERT: A 1136 LYS cc_start: 0.6517 (ptmm) cc_final: 0.6289 (ptmm) REVERT: A 1217 MET cc_start: 0.7517 (mmm) cc_final: 0.6960 (tpp) REVERT: A 1261 HIS cc_start: 0.8072 (m90) cc_final: 0.7782 (p90) outliers start: 33 outliers final: 27 residues processed: 107 average time/residue: 0.0998 time to fit residues: 15.9582 Evaluate side-chains 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 182 PHE Chi-restraints excluded: chain A residue 194 ASP 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 487 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 596 PHE Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 777 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 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 Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4369 r_free = 0.4369 target = 0.139783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.102559 restraints weight = 49278.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.103340 restraints weight = 27389.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.104068 restraints weight = 18773.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.104830 restraints weight = 15399.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.105084 restraints weight = 13533.424| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11541 Z= 0.184 Angle : 0.623 12.142 15790 Z= 0.346 Chirality : 0.042 0.366 1728 Planarity : 0.004 0.040 1786 Dihedral : 18.140 129.589 2126 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.86 % Allowed : 19.74 % 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: -1.02 (0.23), residues: 1167 helix: 0.07 (0.21), residues: 554 sheet: -0.60 (0.57), residues: 86 loop : -1.46 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.019 0.002 TYR A 659 PHE 0.018 0.002 PHE A1240 TRP 0.009 0.002 TRP A1142 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (11541) covalent geometry : angle 0.62282 / 0.35 (15790) hydrogen bonds : bond 0.05208 / 3.36 ( 484) hydrogen bonds : angle 5.07326 / 3.56 ( 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 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7459 (mtm180) REVERT: A 55 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 117 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7721 (tm-30) REVERT: A 182 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (t80) REVERT: A 183 HIS cc_start: 0.7960 (m170) cc_final: 0.7623 (m170) REVERT: A 245 ASP cc_start: 0.8130 (m-30) cc_final: 0.7438 (p0) REVERT: A 895 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8273 (mmmm) REVERT: A 941 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8364 (t80) REVERT: A 1217 MET cc_start: 0.7545 (mmm) cc_final: 0.6976 (tpp) REVERT: A 1261 HIS cc_start: 0.8101 (m90) cc_final: 0.7808 (p90) outliers start: 31 outliers final: 27 residues processed: 103 average time/residue: 0.0922 time to fit residues: 14.0891 Evaluate side-chains 113 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 194 ASP 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 278 ILE Chi-restraints excluded: chain A residue 283 THR 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 633 MET Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 777 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 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 Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.141994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.104804 restraints weight = 49861.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.105484 restraints weight = 27562.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.106204 restraints weight = 18765.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.106959 restraints weight = 15436.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.107138 restraints weight = 13644.812| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11541 Z= 0.129 Angle : 0.588 12.103 15790 Z= 0.325 Chirality : 0.041 0.361 1728 Planarity : 0.004 0.041 1786 Dihedral : 18.039 129.128 2126 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.31 % Allowed : 20.85 % Favored : 76.85 % 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: 0.18 (0.22), residues: 558 sheet: -0.52 (0.56), residues: 86 loop : -1.44 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 186 TYR 0.016 0.001 TYR A 659 PHE 0.019 0.001 PHE A1240 TRP 0.007 0.001 TRP A 808 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11541) covalent geometry : angle 0.58792 / 0.33 (15790) hydrogen bonds : bond 0.04797 / 3.12 ( 484) hydrogen bonds : angle 4.88150 / 3.41 ( 1331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.37 seconds wall clock time: 60 minutes 28.80 seconds (3628.80 seconds total)