Starting phenix.real_space_refine on Wed Aug 5 18:20:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.cif" model { file = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2026/8att_15662.map" } resolution = 3.44 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 59 5.49 5 S 36 5.16 5 C 6931 2.51 5 N 1921 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11124 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2785 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 320} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 7184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7184 Classifications: {'peptide': 906} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 43, 'TRANS': 862} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 505 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNAv2': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.31, per 1000 atoms: 0.21 Number of scatterers: 11124 At special positions: 0 Unit cell: (104.76, 109.61, 119.31, 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 36 16.00 P 59 15.00 O 2177 8.00 N 1921 7.00 C 6931 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: 0.92 Conformation dependent library (CDL) restraints added in 538.9 milliseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 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: 57 helices and 12 sheets defined 58.9% alpha, 9.4% beta 22 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.801A 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 37 through 42 removed outlier: 4.173A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) 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: 3.711A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.987A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.704A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.828A 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: 3.574A 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: 4.048A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 297 through 301 removed outlier: 4.011A pdb=" N LYS B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 408 through 420 removed outlier: 3.706A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 3.618A pdb=" N TRP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 463 - end of helix removed outlier: 3.510A pdb=" N SER A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.840A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix removed outlier: 3.563A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 558 Processing helix chain 'A' and resid 593 through 610 Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.739A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.245A 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 removed outlier: 3.535A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 872 removed outlier: 4.657A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 3.909A pdb=" N HIS A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 removed outlier: 3.515A pdb=" N GLU A 935 " --> pdb=" O ASN A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.053A pdb=" N THR A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1047 through 1066 removed outlier: 3.720A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 removed outlier: 3.630A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1303 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.658A pdb=" N VAL A1342 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.614A pdb=" N VAL B 50 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 76 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 52 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 49 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 133 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS B 167 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N LYS B 131 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 13.433A pdb=" N LEU B 169 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N LEU B 133 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N TRP B 171 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL B 135 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ASN B 137 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 166 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 242 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 207 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 244 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 620 removed outlier: 3.685A pdb=" N ALA A 625 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684 removed outlier: 7.599A pdb=" N TRP A 682 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY A 689 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 684 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 817 through 819 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: 3.516A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.506A 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 945 removed outlier: 3.667A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1185 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.511A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1236 through 1238 531 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3347 1.34 - 1.46: 2025 1.46 - 1.57: 5952 1.57 - 1.69: 108 1.69 - 1.81: 61 Bond restraints: 11493 Sorted by residual: bond pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.20e-02 6.94e+03 1.21e+02 bond pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 1.446 1.552 -0.106 1.00e-02 1.00e+04 1.12e+02 bond pdb=" O3' DA N 129 " pdb=" P DA N 130 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.20e-02 6.94e+03 7.42e+01 bond pdb=" C2' DA N 127 " pdb=" C1' DA N 127 " ideal model delta sigma weight residual 1.518 1.595 -0.077 1.00e-02 1.00e+04 5.86e+01 bond pdb=" O3' DT N 128 " pdb=" P DA N 129 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.20e-02 6.94e+03 3.45e+01 ... (remaining 11488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 15676 3.56 - 7.12: 102 7.12 - 10.68: 12 10.68 - 14.24: 3 14.24 - 17.80: 2 Bond angle restraints: 15795 Sorted by residual: angle pdb=" C3' DG N 126 " pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 119.70 107.37 12.33 1.20e+00 6.94e-01 1.06e+02 angle pdb=" C5' DG N 108 " pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 109.30 127.10 -17.80 1.90e+00 2.77e-01 8.78e+01 angle pdb=" O4' DG N 108 " pdb=" C4' DG N 108 " pdb=" C3' DG N 108 " ideal model delta sigma weight residual 106.00 101.28 4.72 6.00e-01 2.78e+00 6.20e+01 angle pdb=" CA PRO A 621 " pdb=" N PRO A 621 " pdb=" CD PRO A 621 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 angle pdb=" C5' DT T 16 " pdb=" C4' DT T 16 " pdb=" O4' DT T 16 " ideal model delta sigma weight residual 109.30 121.15 -11.85 1.90e+00 2.77e-01 3.89e+01 ... (remaining 15790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 6250 26.43 - 52.87: 484 52.87 - 79.30: 79 79.30 - 105.73: 5 105.73 - 132.17: 1 Dihedral angle restraints: 6819 sinusoidal: 3184 harmonic: 3635 Sorted by residual: dihedral pdb=" C4' GTP C 201 " pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual 260.87 128.71 132.17 1 2.00e+01 2.50e-03 4.01e+01 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 3.46 101.14 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 5.26 64.01 1 2.00e+01 2.50e-03 1.35e+01 ... (remaining 6816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1701 0.129 - 0.259: 24 0.259 - 0.388: 2 0.388 - 0.518: 7 0.518 - 0.647: 11 Chirality restraints: 1745 Sorted by residual: chirality pdb=" P G C 102 " pdb=" OP1 G C 102 " pdb=" OP2 G C 102 " pdb=" O5' G C 102 " both_signs ideal model delta sigma weight residual True 2.17 -2.82 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC T 24 " pdb=" OP1 DC T 24 " pdb=" OP2 DC T 24 " pdb=" O5' DC T 24 " 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=" C3' DA T 19 " pdb=" C4' DA T 19 " pdb=" O3' DA T 19 " pdb=" C2' DA T 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.13 -0.60 2.00e-01 2.50e+01 9.13e+00 ... (remaining 1742 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 620 " 0.068 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO A 621 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 431 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.74e+00 pdb=" CG TRP A 431 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 431 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 431 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 431 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1019 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR A1019 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A1019 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A1020 " 0.011 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 10708 3.24 - 3.79: 17891 3.79 - 4.35: 23515 4.35 - 4.90: 37602 Nonbonded interactions: 89970 Sorted by model distance: nonbonded pdb=" OG SER A1186 " pdb=" O SER A1190 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR B 307 " pdb=" OE1 GLU B 310 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS B 21 " pdb=" O LYS B 240 " model vdw 2.227 3.120 nonbonded pdb=" OG SER A 703 " pdb=" OE1 GLN A 706 " model vdw 2.232 3.040 ... (remaining 89965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.120 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.005 0.132 11494 Z= 0.330 Angle : 0.790 17.800 15795 Z= 0.455 Chirality : 0.073 0.647 1745 Planarity : 0.005 0.097 1822 Dihedral : 17.654 132.167 4465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.63 % 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: 0.87 (0.24), residues: 1238 helix: 1.64 (0.21), residues: 685 sheet: -0.20 (0.50), residues: 106 loop : -0.88 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1063 TYR 0.012 0.001 TYR A 496 PHE 0.024 0.001 PHE A1338 TRP 0.037 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.32 (11493) covalent geometry : angle 0.78973 / 0.45 (15795) hydrogen bonds : bond 0.14420 / 8.88 ( 580) hydrogen bonds : angle 5.88031 / 4.09 ( 1649) Misc. bond : bond 0.09185 / 4.83 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8252 (p0) cc_final: 0.7887 (p0) REVERT: A 544 MET cc_start: 0.7622 (mmt) cc_final: 0.7396 (mmt) REVERT: A 657 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7801 (ptm160) REVERT: A 763 GLU cc_start: 0.6832 (pt0) cc_final: 0.6549 (pt0) REVERT: A 976 GLN cc_start: 0.6395 (mt0) cc_final: 0.5625 (tp-100) REVERT: A 1157 LEU cc_start: 0.6675 (tp) cc_final: 0.6425 (tp) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0866 time to fit residues: 21.4463 Evaluate side-chains 131 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 overall best weight: 4.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** 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 = 0.4214 r_free = 0.4214 target = 0.172942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128626 restraints weight = 16492.291| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.68 r_work: 0.3511 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11494 Z= 0.173 Angle : 0.638 9.013 15795 Z= 0.341 Chirality : 0.046 0.200 1745 Planarity : 0.005 0.045 1822 Dihedral : 19.168 129.230 1995 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.29 % Allowed : 7.18 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1238 helix: 1.57 (0.20), residues: 690 sheet: -0.03 (0.50), residues: 96 loop : -0.79 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 699 TYR 0.030 0.002 TYR B 161 PHE 0.012 0.001 PHE A1041 TRP 0.022 0.002 TRP A 431 HIS 0.005 0.001 HIS A1213 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (11493) covalent geometry : angle 0.63842 / 0.34 (15795) hydrogen bonds : bond 0.04938 / 3.12 ( 580) hydrogen bonds : angle 4.76218 / 3.29 ( 1649) Misc. bond : bond 0.01116 / 0.59 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 ILE cc_start: 0.8603 (mp) cc_final: 0.8314 (mm) REVERT: B 334 MET cc_start: 0.6454 (mmt) cc_final: 0.6223 (mmm) REVERT: A 544 MET cc_start: 0.7828 (mmt) cc_final: 0.7594 (mmt) REVERT: A 657 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8249 (ptm160) REVERT: A 1070 HIS cc_start: 0.7184 (t-90) cc_final: 0.6824 (t70) REVERT: A 1300 PHE cc_start: 0.7170 (m-80) cc_final: 0.6248 (m-80) outliers start: 14 outliers final: 11 residues processed: 156 average time/residue: 0.0846 time to fit residues: 19.7140 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1132 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127173 restraints weight = 16737.265| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.78 r_work: 0.3479 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11494 Z= 0.198 Angle : 0.631 7.852 15795 Z= 0.335 Chirality : 0.045 0.180 1745 Planarity : 0.004 0.045 1822 Dihedral : 19.386 127.124 1995 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.30 % Allowed : 10.67 % Favored : 87.03 % 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 (0.24), residues: 1238 helix: 1.53 (0.20), residues: 685 sheet: -0.73 (0.47), residues: 110 loop : -0.81 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 699 TYR 0.024 0.002 TYR B 83 PHE 0.014 0.002 PHE A 936 TRP 0.022 0.002 TRP A 431 HIS 0.005 0.001 HIS A 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (11493) covalent geometry : angle 0.63138 / 0.33 (15795) hydrogen bonds : bond 0.04940 / 3.12 ( 580) hydrogen bonds : angle 4.66756 / 3.22 ( 1649) Misc. bond : bond 0.00118 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 334 MET cc_start: 0.6482 (mmt) cc_final: 0.6120 (mmm) REVERT: A 544 MET cc_start: 0.7886 (mmt) cc_final: 0.7642 (mmt) REVERT: A 553 LYS cc_start: 0.6192 (pptt) cc_final: 0.5852 (pptt) REVERT: A 1070 HIS cc_start: 0.7310 (t-90) cc_final: 0.6971 (t70) REVERT: A 1300 PHE cc_start: 0.7055 (m-80) cc_final: 0.6017 (m-80) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.0980 time to fit residues: 22.6932 Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 HIS ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.170363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.128827 restraints weight = 16767.855| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.53 r_work: 0.3489 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11494 Z= 0.171 Angle : 0.607 7.853 15795 Z= 0.321 Chirality : 0.043 0.156 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.308 126.024 1995 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.48 % Allowed : 12.88 % Favored : 84.64 % 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: 0.80 (0.24), residues: 1238 helix: 1.60 (0.20), residues: 683 sheet: -0.48 (0.49), residues: 101 loop : -0.87 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 797 TYR 0.029 0.002 TYR B 161 PHE 0.011 0.001 PHE A1338 TRP 0.017 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (11493) covalent geometry : angle 0.60729 / 0.32 (15795) hydrogen bonds : bond 0.04552 / 2.90 ( 580) hydrogen bonds : angle 4.53492 / 3.12 ( 1649) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 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: 27 poor density : 139 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7864 (mmt) cc_final: 0.7629 (mmt) REVERT: A 553 LYS cc_start: 0.6185 (pptt) cc_final: 0.5860 (pptt) REVERT: A 1070 HIS cc_start: 0.7076 (t70) cc_final: 0.6786 (t70) REVERT: A 1300 PHE cc_start: 0.6932 (m-80) cc_final: 0.5943 (m-80) outliers start: 27 outliers final: 22 residues processed: 153 average time/residue: 0.0928 time to fit residues: 21.2086 Evaluate side-chains 157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.168108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125606 restraints weight = 16784.086| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.88 r_work: 0.3420 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11494 Z= 0.226 Angle : 0.646 8.030 15795 Z= 0.341 Chirality : 0.045 0.190 1745 Planarity : 0.005 0.045 1822 Dihedral : 19.356 124.467 1995 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.22 % Allowed : 13.80 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1238 helix: 1.46 (0.20), residues: 684 sheet: -0.56 (0.48), residues: 103 loop : -1.02 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1250 TYR 0.032 0.002 TYR B 161 PHE 0.014 0.002 PHE A1338 TRP 0.021 0.002 TRP A 431 HIS 0.006 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (11493) covalent geometry : angle 0.64628 / 0.34 (15795) hydrogen bonds : bond 0.04844 / 3.06 ( 580) hydrogen bonds : angle 4.63516 / 3.19 ( 1649) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 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: 35 poor density : 137 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 544 MET cc_start: 0.7905 (mmt) cc_final: 0.7678 (mmt) REVERT: A 553 LYS cc_start: 0.6187 (pptt) cc_final: 0.5890 (pptt) REVERT: A 1070 HIS cc_start: 0.7147 (t70) cc_final: 0.6836 (t70) REVERT: A 1250 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8516 (mmm160) REVERT: A 1300 PHE cc_start: 0.6973 (m-80) cc_final: 0.5915 (m-80) outliers start: 35 outliers final: 29 residues processed: 162 average time/residue: 0.0893 time to fit residues: 21.6766 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1249 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 50.0000 chunk 86 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4178 r_free = 0.4178 target = 0.170531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129652 restraints weight = 16809.892| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.59 r_work: 0.3482 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11494 Z= 0.141 Angle : 0.600 7.902 15795 Z= 0.315 Chirality : 0.042 0.173 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.246 123.959 1995 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.13 % Allowed : 14.54 % Favored : 82.34 % 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: 0.92 (0.24), residues: 1238 helix: 1.71 (0.20), residues: 685 sheet: -0.43 (0.49), residues: 103 loop : -0.85 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1240 TYR 0.040 0.002 TYR B 161 PHE 0.024 0.001 PHE A1338 TRP 0.013 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11493) covalent geometry : angle 0.60044 / 0.31 (15795) hydrogen bonds : bond 0.04240 / 2.68 ( 580) hydrogen bonds : angle 4.43355 / 3.05 ( 1649) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 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: 34 poor density : 143 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 29 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: A 544 MET cc_start: 0.7925 (mmt) cc_final: 0.7705 (mmt) REVERT: A 553 LYS cc_start: 0.6208 (pptt) cc_final: 0.5955 (pptt) REVERT: A 675 MET cc_start: 0.7856 (mtp) cc_final: 0.7631 (mtm) REVERT: A 1070 HIS cc_start: 0.7086 (t70) cc_final: 0.6814 (t70) REVERT: A 1250 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8480 (mmm160) REVERT: A 1300 PHE cc_start: 0.6943 (m-80) cc_final: 0.5844 (m-80) outliers start: 34 outliers final: 23 residues processed: 163 average time/residue: 0.0815 time to fit residues: 20.1281 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 449 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4145 r_free = 0.4145 target = 0.167559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125682 restraints weight = 16848.369| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.71 r_work: 0.3417 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11494 Z= 0.230 Angle : 0.669 8.568 15795 Z= 0.350 Chirality : 0.045 0.205 1745 Planarity : 0.005 0.043 1822 Dihedral : 19.337 121.873 1995 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.77 % Allowed : 15.18 % Favored : 81.05 % 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 (0.24), residues: 1238 helix: 1.49 (0.20), residues: 683 sheet: -0.52 (0.48), residues: 106 loop : -1.00 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 989 TYR 0.043 0.003 TYR B 161 PHE 0.026 0.002 PHE A1338 TRP 0.022 0.002 TRP A 431 HIS 0.006 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (11493) covalent geometry : angle 0.66933 / 0.35 (15795) hydrogen bonds : bond 0.04957 / 3.11 ( 580) hydrogen bonds : angle 4.62557 / 3.18 ( 1649) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8107 (tt0) cc_final: 0.7449 (tt0) REVERT: A 544 MET cc_start: 0.7959 (mmt) cc_final: 0.7712 (mmt) REVERT: A 553 LYS cc_start: 0.6197 (pptt) cc_final: 0.5893 (pptt) REVERT: A 673 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7834 (pp) REVERT: A 1070 HIS cc_start: 0.7230 (t70) cc_final: 0.6953 (t70) REVERT: A 1250 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8467 (mmm160) REVERT: A 1300 PHE cc_start: 0.7080 (m-80) cc_final: 0.5989 (m-80) outliers start: 41 outliers final: 30 residues processed: 166 average time/residue: 0.0821 time to fit residues: 20.4477 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1131 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4158 r_free = 0.4158 target = 0.168873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127738 restraints weight = 16867.161| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.58 r_work: 0.3450 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11494 Z= 0.182 Angle : 0.644 8.460 15795 Z= 0.334 Chirality : 0.044 0.192 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.310 121.314 1995 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.40 % Allowed : 15.92 % Favored : 80.68 % 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: 0.73 (0.24), residues: 1238 helix: 1.57 (0.20), residues: 685 sheet: -0.47 (0.48), residues: 106 loop : -0.96 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.025 0.002 TYR A1348 PHE 0.027 0.001 PHE A1338 TRP 0.016 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11493) covalent geometry : angle 0.64433 / 0.33 (15795) hydrogen bonds : bond 0.04484 / 2.80 ( 580) hydrogen bonds : angle 4.55593 / 3.13 ( 1649) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8117 (tt0) cc_final: 0.7445 (tt0) REVERT: B 214 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8481 (pttm) REVERT: B 246 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7718 (tt0) REVERT: A 544 MET cc_start: 0.7936 (mmt) cc_final: 0.7692 (mmt) REVERT: A 553 LYS cc_start: 0.6202 (pptt) cc_final: 0.5955 (pptt) REVERT: A 673 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7790 (pp) REVERT: A 675 MET cc_start: 0.7891 (mtp) cc_final: 0.7614 (mtm) REVERT: A 1070 HIS cc_start: 0.7380 (t70) cc_final: 0.7072 (t70) REVERT: A 1250 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8424 (mmm160) REVERT: A 1300 PHE cc_start: 0.7108 (m-80) cc_final: 0.5976 (m-80) outliers start: 37 outliers final: 31 residues processed: 164 average time/residue: 0.0840 time to fit residues: 20.7102 Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1131 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 694 GLN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4193 r_free = 0.4193 target = 0.171790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131219 restraints weight = 16630.919| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.57 r_work: 0.3505 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11494 Z= 0.124 Angle : 0.601 10.475 15795 Z= 0.311 Chirality : 0.042 0.190 1745 Planarity : 0.004 0.045 1822 Dihedral : 19.122 119.112 1995 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.58 % Allowed : 17.30 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1238 helix: 1.82 (0.20), residues: 686 sheet: -0.36 (0.48), residues: 110 loop : -0.76 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 827 TYR 0.018 0.002 TYR B 83 PHE 0.026 0.001 PHE A1338 TRP 0.012 0.001 TRP A 734 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11493) covalent geometry : angle 0.60092 / 0.31 (15795) hydrogen bonds : bond 0.03881 / 2.44 ( 580) hydrogen bonds : angle 4.33576 / 2.98 ( 1649) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7922 (mmt) cc_final: 0.7686 (mmt) REVERT: A 553 LYS cc_start: 0.6231 (pptt) cc_final: 0.6017 (pptt) REVERT: A 673 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 675 MET cc_start: 0.7580 (mtp) cc_final: 0.7377 (mtm) REVERT: A 1070 HIS cc_start: 0.7350 (t70) cc_final: 0.7029 (t70) REVERT: A 1250 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8376 (mmm160) REVERT: A 1300 PHE cc_start: 0.7151 (m-80) cc_final: 0.6026 (m-80) outliers start: 28 outliers final: 26 residues processed: 166 average time/residue: 0.0841 time to fit residues: 20.8788 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4164 r_free = 0.4164 target = 0.169147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128072 restraints weight = 16880.197| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.62 r_work: 0.3459 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11494 Z= 0.186 Angle : 0.644 10.253 15795 Z= 0.331 Chirality : 0.044 0.180 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.195 118.039 1995 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.58 % Allowed : 17.48 % Favored : 79.94 % 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: 0.88 (0.24), residues: 1238 helix: 1.68 (0.20), residues: 685 sheet: -0.36 (0.48), residues: 110 loop : -0.89 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 883 TYR 0.024 0.002 TYR B 83 PHE 0.026 0.002 PHE A1338 TRP 0.017 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (11493) covalent geometry : angle 0.64376 / 0.33 (15795) hydrogen bonds : bond 0.04360 / 2.71 ( 580) hydrogen bonds : angle 4.49277 / 3.08 ( 1649) Misc. bond : bond 0.00080 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7956 (mmt) cc_final: 0.7728 (mmt) REVERT: A 553 LYS cc_start: 0.6251 (pptt) cc_final: 0.6024 (pptt) REVERT: A 673 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7678 (pp) REVERT: A 675 MET cc_start: 0.7770 (mtp) cc_final: 0.7532 (mtm) REVERT: A 1070 HIS cc_start: 0.7267 (t70) cc_final: 0.6964 (t70) REVERT: A 1250 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8405 (mmm160) REVERT: A 1300 PHE cc_start: 0.7128 (m-80) cc_final: 0.5962 (m-80) outliers start: 28 outliers final: 25 residues processed: 157 average time/residue: 0.0897 time to fit residues: 20.7962 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** 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 = 0.4162 r_free = 0.4162 target = 0.169005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127690 restraints weight = 16961.944| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.64 r_work: 0.3451 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11494 Z= 0.181 Angle : 0.637 9.663 15795 Z= 0.329 Chirality : 0.044 0.180 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.248 117.137 1995 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.85 % Allowed : 17.11 % Favored : 80.04 % 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 (0.24), residues: 1238 helix: 1.62 (0.20), residues: 685 sheet: -0.22 (0.49), residues: 106 loop : -0.94 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 883 TYR 0.024 0.002 TYR B 83 PHE 0.026 0.002 PHE A1338 TRP 0.017 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11493) covalent geometry : angle 0.63652 / 0.33 (15795) hydrogen bonds : bond 0.04372 / 2.71 ( 580) hydrogen bonds : angle 4.48617 / 3.09 ( 1649) Misc. bond : bond 0.00081 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.83 seconds wall clock time: 38 minutes 31.80 seconds (2311.80 seconds total)