Starting phenix.real_space_refine on Fri Jul 3 01:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2026/8q63_18183.cif" } resolution = 3.68 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= 0.010 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 70 5.49 5 S 35 5.16 5 C 7041 2.51 5 N 1971 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 11346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2698 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7200 Classifications: {'peptide': 915} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 44, 'TRANS': 870} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "N" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 642 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "T" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 152 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 2.41, per 1000 atoms: 0.21 Number of scatterers: 11346 At special positions: 0 Unit cell: (103.79, 116.4, 118.34, 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 35 16.00 P 70 15.00 O 2229 8.00 N 1971 7.00 C 7041 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 416.2 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 59.8% alpha, 7.3% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.890A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.762A pdb=" N GLU B 47 " --> pdb=" O HIS B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.834A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.960A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.729A pdb=" N GLY B 164 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.521A pdb=" N GLU B 212 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.297A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.141A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.573A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 4.247A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 448 through 476 removed outlier: 4.518A pdb=" N VAL A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.764A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 removed outlier: 4.529A pdb=" N GLY A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.855A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 611 removed outlier: 3.747A pdb=" N VAL A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 663 removed outlier: 3.628A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.884A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 737 through 751 Processing helix chain 'A' and resid 777 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 removed outlier: 3.703A pdb=" N ALA A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 997 Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.729A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1046 through 1066 removed outlier: 4.435A pdb=" N PHE A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A1060 " --> pdb=" O LYS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 4.066A pdb=" N LYS A1094 " --> pdb=" O ASP A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1197 through 1213 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1244 No H-bonds generated for 'chain 'A' and resid 1242 through 1244' Processing helix chain 'A' and resid 1245 through 1260 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.647A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A1281 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1301 removed outlier: 3.774A pdb=" N LEU A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A1300 " --> pdb=" O THR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1339 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.704A pdb=" N VAL B 135 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B 247 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.953A pdb=" N ILE B 207 " --> pdb=" O ILE B 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530 removed outlier: 3.547A pdb=" N ALA A 635 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.997A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 938 " --> pdb=" O LYS A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 removed outlier: 3.739A pdb=" N TRP A1110 " --> pdb=" O ILE A1118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.610A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1999 1.33 - 1.45: 3277 1.45 - 1.57: 6274 1.57 - 1.69: 146 1.69 - 1.82: 60 Bond restraints: 11756 Sorted by residual: bond pdb=" C3' DC N 137 " pdb=" C2' DC N 137 " ideal model delta sigma weight residual 1.516 1.696 -0.180 8.00e-03 1.56e+04 5.04e+02 bond pdb=" C3' DT N 111 " pdb=" C2' DT N 111 " ideal model delta sigma weight residual 1.516 1.632 -0.116 8.00e-03 1.56e+04 2.09e+02 bond pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " ideal model delta sigma weight residual 1.518 1.409 0.109 1.00e-02 1.00e+04 1.18e+02 bond pdb=" O3' DG N 136 " pdb=" P DC N 137 " ideal model delta sigma weight residual 1.607 1.449 0.158 1.50e-02 4.44e+03 1.11e+02 bond pdb=" C3' DA T 30 " pdb=" C2' DA T 30 " ideal model delta sigma weight residual 1.516 1.597 -0.081 8.00e-03 1.56e+04 1.03e+02 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 16024 4.16 - 8.32: 177 8.32 - 12.48: 18 12.48 - 16.64: 6 16.64 - 20.80: 2 Bond angle restraints: 16227 Sorted by residual: angle pdb=" O3' DG N 136 " pdb=" P DC N 137 " pdb=" O5' DC N 137 " ideal model delta sigma weight residual 104.00 124.80 -20.80 1.50e+00 4.44e-01 1.92e+02 angle pdb=" C3' DC T 18 " pdb=" O3' DC T 18 " pdb=" P DA T 19 " ideal model delta sigma weight residual 120.20 104.85 15.35 1.50e+00 4.44e-01 1.05e+02 angle pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " pdb=" N1 DC N 137 " ideal model delta sigma weight residual 114.30 100.28 14.02 1.40e+00 5.10e-01 1.00e+02 angle pdb=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 120.20 105.74 14.46 1.50e+00 4.44e-01 9.29e+01 angle pdb=" C3' DA N 131 " pdb=" O3' DA N 131 " pdb=" P DA N 132 " ideal model delta sigma weight residual 120.20 132.94 -12.74 1.50e+00 4.44e-01 7.22e+01 ... (remaining 16222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 6538 34.16 - 68.31: 354 68.31 - 102.47: 16 102.47 - 136.62: 1 136.62 - 170.78: 2 Dihedral angle restraints: 6911 sinusoidal: 3280 harmonic: 3631 Sorted by residual: dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -12.75 117.34 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" C5' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" O3' G C 108 " ideal model delta sinusoidal sigma weight residual 147.00 112.01 34.99 1 8.00e+00 1.56e-02 2.71e+01 dihedral pdb=" O4' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 24.00 -7.29 31.29 1 8.00e+00 1.56e-02 2.18e+01 ... (remaining 6908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1713 0.129 - 0.257: 39 0.257 - 0.386: 4 0.386 - 0.515: 17 0.515 - 0.644: 27 Chirality restraints: 1800 Sorted by residual: chirality pdb=" P DG T 10 " pdb=" OP1 DG T 10 " pdb=" OP2 DG T 10 " pdb=" O5' DG T 10 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG N 108 " pdb=" OP1 DG N 108 " pdb=" OP2 DG N 108 " pdb=" O5' DG N 108 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.10e+00 chirality pdb=" P DC N 137 " pdb=" OP1 DC N 137 " pdb=" OP2 DC N 137 " pdb=" O5' DC N 137 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.87e+00 ... (remaining 1797 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 135 " 0.034 2.00e-02 2.50e+03 1.68e-02 7.09e+00 pdb=" N1 DT N 135 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT N 135 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DT N 135 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT N 135 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT N 135 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT N 135 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT N 135 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 159 " 0.017 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP B 159 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 159 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 159 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 159 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 159 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 159 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 320 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU B 320 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 320 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 321 " -0.011 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 285 2.68 - 3.23: 11044 3.23 - 3.79: 18562 3.79 - 4.34: 24480 4.34 - 4.90: 38376 Nonbonded interactions: 92747 Sorted by model distance: nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.121 3.040 nonbonded pdb=" OD1 ASP A 843 " pdb=" NE2 GLN A 916 " model vdw 2.205 3.120 nonbonded pdb=" O SER B 190 " pdb=" OG SER B 193 " model vdw 2.228 3.040 nonbonded pdb=" N LYS B 49 " pdb=" O LYS B 131 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP A 876 " pdb=" NH1 ARG A 883 " model vdw 2.264 3.120 ... (remaining 92742 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.007 0.180 11757 Z= 0.576 Angle : 1.047 20.795 16227 Z= 0.597 Chirality : 0.096 0.644 1800 Planarity : 0.004 0.042 1825 Dihedral : 18.308 170.778 4557 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.09 % Allowed : 0.66 % Favored : 99.25 % 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: 0.60 (0.25), residues: 1232 helix: 1.59 (0.21), residues: 666 sheet: -1.19 (0.56), residues: 80 loop : -1.01 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 989 TYR 0.020 0.002 TYR A 954 PHE 0.028 0.002 PHE A 936 TRP 0.043 0.002 TRP B 159 HIS 0.013 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.58 (11756) covalent geometry : angle 1.04669 / 0.60 (16227) hydrogen bonds : bond 0.15627 / 10.42 ( 586) hydrogen bonds : angle 6.37006 / 4.41 ( 1642) Misc. bond : bond 0.01190 / 0.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 ASN cc_start: 0.7988 (m-40) cc_final: 0.7540 (m110) REVERT: A 796 ASP cc_start: 0.8051 (m-30) cc_final: 0.7791 (m-30) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.0969 time to fit residues: 25.5753 Evaluate side-chains 128 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 642 ASN ** A 925 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.148604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115072 restraints weight = 20621.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.119038 restraints weight = 11059.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121631 restraints weight = 7613.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.123175 restraints weight = 6079.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.124135 restraints weight = 5326.712| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11757 Z= 0.239 Angle : 0.724 9.169 16227 Z= 0.387 Chirality : 0.047 0.287 1800 Planarity : 0.005 0.105 1825 Dihedral : 19.262 179.472 2142 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.50 % Allowed : 9.48 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1232 helix: 1.27 (0.20), residues: 679 sheet: -1.04 (0.58), residues: 74 loop : -1.10 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 883 TYR 0.028 0.002 TYR A 496 PHE 0.034 0.002 PHE A 754 TRP 0.024 0.002 TRP B 159 HIS 0.008 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 (11756) covalent geometry : angle 0.72374 / 0.39 (16227) hydrogen bonds : bond 0.06237 / 4.25 ( 586) hydrogen bonds : angle 4.98898 / 3.51 ( 1642) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7187 (ptm160) REVERT: A 796 ASP cc_start: 0.8095 (m-30) cc_final: 0.7804 (m-30) REVERT: A 856 LYS cc_start: 0.7264 (mmmt) cc_final: 0.7023 (mmmt) outliers start: 16 outliers final: 10 residues processed: 158 average time/residue: 0.0802 time to fit residues: 19.0110 Evaluate side-chains 152 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 50.0000 chunk 58 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 0.0470 chunk 83 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4144 r_free = 0.4144 target = 0.154149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.122476 restraints weight = 20720.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126555 restraints weight = 11065.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129186 restraints weight = 7555.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130966 restraints weight = 5970.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131907 restraints weight = 5140.145| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11757 Z= 0.141 Angle : 0.624 7.666 16227 Z= 0.333 Chirality : 0.043 0.297 1800 Planarity : 0.004 0.046 1825 Dihedral : 18.986 178.449 2142 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 11.83 % Favored : 85.73 % 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: 0.62 (0.25), residues: 1232 helix: 1.60 (0.20), residues: 669 sheet: -0.83 (0.59), residues: 74 loop : -1.07 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 530 TYR 0.030 0.002 TYR A 496 PHE 0.028 0.002 PHE A 936 TRP 0.027 0.001 TRP B 159 HIS 0.005 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11756) covalent geometry : angle 0.62380 / 0.33 (16227) hydrogen bonds : bond 0.04893 / 3.38 ( 586) hydrogen bonds : angle 4.48828 / 3.16 ( 1642) Misc. bond : bond 0.00073 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7941 (tt) REVERT: B 321 TRP cc_start: 0.8050 (t60) cc_final: 0.7492 (t60) REVERT: A 656 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9054 (tt) REVERT: A 727 ASN cc_start: 0.7831 (m-40) cc_final: 0.7348 (m110) REVERT: A 796 ASP cc_start: 0.7984 (m-30) cc_final: 0.7751 (m-30) REVERT: A 856 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6746 (mmmt) REVERT: A 1140 SER cc_start: 0.8599 (p) cc_final: 0.8394 (p) REVERT: A 1201 MET cc_start: 0.7822 (ttp) cc_final: 0.7442 (ttp) outliers start: 26 outliers final: 13 residues processed: 176 average time/residue: 0.1000 time to fit residues: 26.1998 Evaluate side-chains 164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 0.0370 chunk 24 optimal weight: 7.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.148563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114632 restraints weight = 20818.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.118594 restraints weight = 11230.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121192 restraints weight = 7777.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.122696 restraints weight = 6219.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.123766 restraints weight = 5463.498| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11757 Z= 0.212 Angle : 0.654 8.405 16227 Z= 0.347 Chirality : 0.044 0.343 1800 Planarity : 0.005 0.054 1825 Dihedral : 18.987 175.285 2142 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.10 % Allowed : 14.65 % Favored : 82.25 % 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: 0.48 (0.25), residues: 1232 helix: 1.45 (0.20), residues: 674 sheet: -0.95 (0.58), residues: 74 loop : -1.08 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 533 TYR 0.025 0.002 TYR A 496 PHE 0.023 0.002 PHE B 132 TRP 0.029 0.002 TRP B 159 HIS 0.006 0.001 HIS A1188 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (11756) covalent geometry : angle 0.65442 / 0.35 (16227) hydrogen bonds : bond 0.05188 / 3.52 ( 586) hydrogen bonds : angle 4.62793 / 3.25 ( 1642) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 TRP cc_start: 0.7876 (t60) cc_final: 0.7208 (t60) REVERT: B 228 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 796 ASP cc_start: 0.8077 (m-30) cc_final: 0.7839 (m-30) REVERT: A 1140 SER cc_start: 0.8687 (p) cc_final: 0.8479 (p) outliers start: 33 outliers final: 20 residues processed: 167 average time/residue: 0.0994 time to fit residues: 25.0948 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 10.0000 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4119 r_free = 0.4119 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.117415 restraints weight = 20460.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121433 restraints weight = 10961.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124119 restraints weight = 7556.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125695 restraints weight = 6012.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126806 restraints weight = 5255.602| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11757 Z= 0.151 Angle : 0.633 9.426 16227 Z= 0.331 Chirality : 0.043 0.272 1800 Planarity : 0.004 0.044 1825 Dihedral : 18.867 172.448 2142 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.44 % Allowed : 16.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1232 helix: 1.56 (0.20), residues: 674 sheet: -0.84 (0.59), residues: 74 loop : -1.00 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 533 TYR 0.041 0.002 TYR B 29 PHE 0.037 0.002 PHE A 936 TRP 0.025 0.002 TRP B 159 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11756) covalent geometry : angle 0.63252 / 0.33 (16227) hydrogen bonds : bond 0.04734 / 3.26 ( 586) hydrogen bonds : angle 4.43724 / 3.11 ( 1642) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7381 (tp) cc_final: 0.7169 (mt) REVERT: B 321 TRP cc_start: 0.7990 (t60) cc_final: 0.7298 (t60) REVERT: A 796 ASP cc_start: 0.8055 (m-30) cc_final: 0.7824 (m-30) REVERT: A 926 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 1140 SER cc_start: 0.8675 (p) cc_final: 0.8463 (p) REVERT: A 1201 MET cc_start: 0.7735 (ttp) cc_final: 0.7428 (ttp) outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 0.0939 time to fit residues: 24.9024 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4093 r_free = 0.4093 target = 0.148927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115316 restraints weight = 20667.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119267 restraints weight = 11207.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121804 restraints weight = 7751.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.123482 restraints weight = 6211.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.124438 restraints weight = 5406.674| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 11757 Z= 0.198 Angle : 0.663 11.315 16227 Z= 0.346 Chirality : 0.044 0.262 1800 Planarity : 0.004 0.041 1825 Dihedral : 18.928 169.551 2142 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % 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: 0.54 (0.25), residues: 1232 helix: 1.46 (0.21), residues: 673 sheet: -0.86 (0.59), residues: 74 loop : -1.01 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.043 0.002 TYR B 29 PHE 0.026 0.002 PHE B 132 TRP 0.044 0.002 TRP B 159 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (11756) covalent geometry : angle 0.66263 / 0.35 (16227) hydrogen bonds : bond 0.04959 / 3.36 ( 586) hydrogen bonds : angle 4.58467 / 3.20 ( 1642) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 296 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7773 (mmmt) REVERT: B 321 TRP cc_start: 0.8074 (t60) cc_final: 0.7362 (t60) REVERT: A 656 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 796 ASP cc_start: 0.8079 (m-30) cc_final: 0.7856 (m-30) REVERT: A 926 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 1140 SER cc_start: 0.8720 (p) cc_final: 0.8497 (p) outliers start: 27 outliers final: 21 residues processed: 161 average time/residue: 0.0857 time to fit residues: 21.0270 Evaluate side-chains 156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4108 r_free = 0.4108 target = 0.150074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116432 restraints weight = 20454.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120454 restraints weight = 11055.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123097 restraints weight = 7616.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124738 restraints weight = 6068.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.125303 restraints weight = 5283.318| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 11757 Z= 0.165 Angle : 0.645 10.591 16227 Z= 0.335 Chirality : 0.043 0.278 1800 Planarity : 0.004 0.038 1825 Dihedral : 18.870 168.733 2142 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.72 % Allowed : 17.37 % Favored : 79.91 % 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: 0.59 (0.25), residues: 1232 helix: 1.43 (0.20), residues: 680 sheet: -0.81 (0.59), residues: 74 loop : -0.89 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.035 0.002 TYR B 29 PHE 0.032 0.002 PHE B 132 TRP 0.058 0.002 TRP B 159 HIS 0.004 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (11756) covalent geometry : angle 0.64515 / 0.34 (16227) hydrogen bonds : bond 0.04740 / 3.23 ( 586) hydrogen bonds : angle 4.49024 / 3.14 ( 1642) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7276 (m-10) cc_final: 0.7063 (m-10) REVERT: B 159 TRP cc_start: 0.7973 (t60) cc_final: 0.7299 (t60) REVERT: B 296 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7784 (mmmt) REVERT: B 321 TRP cc_start: 0.8012 (t60) cc_final: 0.7354 (t60) REVERT: A 656 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8902 (tt) REVERT: A 796 ASP cc_start: 0.8021 (m-30) cc_final: 0.7800 (m-30) REVERT: A 1140 SER cc_start: 0.8721 (p) cc_final: 0.8488 (p) REVERT: A 1201 MET cc_start: 0.7681 (ttp) cc_final: 0.7439 (ttp) outliers start: 29 outliers final: 22 residues processed: 160 average time/residue: 0.0890 time to fit residues: 21.9690 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 35 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4124 r_free = 0.4124 target = 0.151543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118092 restraints weight = 20434.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.122117 restraints weight = 10950.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124825 restraints weight = 7513.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126497 restraints weight = 5963.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127527 restraints weight = 5178.847| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 11757 Z= 0.147 Angle : 0.641 11.885 16227 Z= 0.330 Chirality : 0.043 0.280 1800 Planarity : 0.004 0.037 1825 Dihedral : 18.756 170.914 2142 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.54 % Allowed : 18.31 % Favored : 79.15 % 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: 0.66 (0.25), residues: 1232 helix: 1.50 (0.21), residues: 675 sheet: -0.70 (0.60), residues: 74 loop : -0.88 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.025 0.002 TYR A 954 PHE 0.031 0.001 PHE B 132 TRP 0.036 0.002 TRP B 159 HIS 0.004 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11756) covalent geometry : angle 0.64071 / 0.33 (16227) hydrogen bonds : bond 0.04502 / 3.07 ( 586) hydrogen bonds : angle 4.42407 / 3.09 ( 1642) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: B 296 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7769 (mmmt) REVERT: B 321 TRP cc_start: 0.7943 (t60) cc_final: 0.7329 (t60) REVERT: A 796 ASP cc_start: 0.7981 (m-30) cc_final: 0.7771 (m-30) REVERT: A 1201 MET cc_start: 0.7622 (ttp) cc_final: 0.7291 (ttp) outliers start: 27 outliers final: 24 residues processed: 164 average time/residue: 0.0969 time to fit residues: 23.9032 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 89 optimal weight: 7.9990 chunk 123 optimal weight: 50.0000 chunk 81 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4102 r_free = 0.4102 target = 0.149581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116242 restraints weight = 20324.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120177 restraints weight = 10996.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.122732 restraints weight = 7609.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124417 restraints weight = 6089.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125319 restraints weight = 5299.073| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11757 Z= 0.184 Angle : 0.671 12.874 16227 Z= 0.344 Chirality : 0.043 0.273 1800 Planarity : 0.004 0.060 1825 Dihedral : 18.788 171.541 2142 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.72 % Allowed : 18.97 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1232 helix: 1.38 (0.21), residues: 681 sheet: -0.54 (0.61), residues: 72 loop : -0.89 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 906 TYR 0.032 0.002 TYR A 954 PHE 0.031 0.002 PHE B 132 TRP 0.043 0.002 TRP B 159 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11756) covalent geometry : angle 0.67080 / 0.34 (16227) hydrogen bonds : bond 0.04745 / 3.20 ( 586) hydrogen bonds : angle 4.53611 / 3.17 ( 1642) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7380 (mmm-85) REVERT: B 296 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7787 (mmmt) REVERT: B 321 TRP cc_start: 0.7961 (t60) cc_final: 0.7341 (t60) REVERT: A 796 ASP cc_start: 0.8003 (m-30) cc_final: 0.7795 (m-30) REVERT: A 926 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 936 PHE cc_start: 0.7645 (t80) cc_final: 0.7440 (t80) REVERT: A 1201 MET cc_start: 0.7705 (ttp) cc_final: 0.7403 (ttp) outliers start: 29 outliers final: 25 residues processed: 160 average time/residue: 0.0936 time to fit residues: 22.7584 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 chunk 124 optimal weight: 50.0000 chunk 117 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 84 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 691 HIS ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.151284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117944 restraints weight = 20331.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121962 restraints weight = 10884.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124601 restraints weight = 7472.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126234 restraints weight = 5940.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127107 restraints weight = 5161.170| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11757 Z= 0.148 Angle : 0.656 12.930 16227 Z= 0.335 Chirality : 0.042 0.278 1800 Planarity : 0.004 0.065 1825 Dihedral : 18.724 172.159 2142 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.25 % Allowed : 19.25 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1232 helix: 1.41 (0.21), residues: 682 sheet: -0.36 (0.61), residues: 72 loop : -0.84 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.024 0.002 TYR A 954 PHE 0.031 0.002 PHE B 132 TRP 0.035 0.002 TRP B 159 HIS 0.003 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11756) covalent geometry : angle 0.65603 / 0.34 (16227) hydrogen bonds : bond 0.04486 / 3.06 ( 586) hydrogen bonds : angle 4.47128 / 3.12 ( 1642) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7137 (m-10) cc_final: 0.6914 (m-10) REVERT: B 296 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7774 (mmmt) REVERT: B 321 TRP cc_start: 0.7941 (t60) cc_final: 0.7334 (t60) REVERT: A 796 ASP cc_start: 0.7998 (m-30) cc_final: 0.7792 (m-30) REVERT: A 926 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 1201 MET cc_start: 0.7674 (ttp) cc_final: 0.7348 (ttp) outliers start: 24 outliers final: 23 residues processed: 155 average time/residue: 0.0947 time to fit residues: 22.2109 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 102 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 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 = 0.4090 r_free = 0.4090 target = 0.148669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115091 restraints weight = 20619.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118952 restraints weight = 11154.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.121536 restraints weight = 7740.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.123193 restraints weight = 6182.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124056 restraints weight = 5377.478| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11757 Z= 0.203 Angle : 0.692 15.023 16227 Z= 0.354 Chirality : 0.044 0.270 1800 Planarity : 0.005 0.058 1825 Dihedral : 18.806 172.172 2142 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.44 % Allowed : 19.15 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1232 helix: 1.30 (0.21), residues: 682 sheet: -0.42 (0.60), residues: 72 loop : -0.94 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.030 0.002 TYR A 954 PHE 0.030 0.002 PHE B 132 TRP 0.065 0.002 TRP B 159 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (11756) covalent geometry : angle 0.69204 / 0.35 (16227) hydrogen bonds : bond 0.04941 / 3.31 ( 586) hydrogen bonds : angle 4.65232 / 3.25 ( 1642) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.50 seconds wall clock time: 33 minutes 39.39 seconds (2019.39 seconds total)